diff --git a/searchindex.js b/searchindex.js index 1a42e5a..35e9ae9 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"API Reference": [[0, "api-reference"]], "Coding guidelines": [[1, "coding-guidelines"]], "Contents:": [[2, null]], "Contributing": [[3, "contributing"]], "Contributing to cycquery": [[1, "contributing-to-cycquery"]], "Example 1. Get all female patients discharged in 2014 (limit to 100 rows).": [[64, "Example-1.-Get-all-female-patients-discharged-in-2014-(limit-to-100-rows)."]], "Example 1. Get all male patients with a mortality outcome.": [[66, "Example-1.-Get-all-male-patients-with-a-mortality-outcome."]], "Example 1. Get all patient admissions from 2021 or later (approx year of admission)": [[67, "Example-1.-Get-all-patient-admissions-from-2021-or-later-(approx-year-of-admission)"]], "Example 1. Get all patient visits in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-in-or-after-2010."]], "Example 1. Get all patient visits that ended in a mortality outcome in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-that-ended-in-a-mortality-outcome-in-or-after-2010."]], "Example 1a. Create a table with only one hospitalization per patient, keeping the most recent encounter for each patient. Sort the dataset by patient_id_hashed and discharge_date_time, and then keep the recent record.": [[65, "Example-1a.-Create-a-table-with-only-one-hospitalization-per-patient,-keeping-the-most-recent-encounter-for-each-patient.-Sort-the-dataset-by-patient_id_hashed-and-discharge_date_time,-and-then-keep-the-recent-record."]], "Example 1b. From the above set of encounters, take a subset of patients who were discharged between April 1, 2015 and March 31, 2016.": [[65, "Example-1b.-From-the-above-set-of-encounters,-take-a-subset-of-patients-who-were-discharged-between-April-1,-2015-and-March-31,-2016."]], "Example 1c. From the above set of encounters, get the total number of admissions for each hospital.": [[65, "Example-1c.-From-the-above-set-of-encounters,-get-the-total-number-of-admissions-for-each-hospital."]], "Example 2. Get all female patient encounters with diagnoses (gastroenteritis in ICD-9 long title).": [[66, "Example-2.-Get-all-female-patient-encounters-with-diagnoses-(gastroenteritis-in-ICD-9-long-title)."]], "Example 2. Get all measurements for female patient visits with sepsis diagnoses, that ended in a mortality outcome.": [[68, "Example-2.-Get-all-measurements-for-female-patient-visits-with-sepsis-diagnoses,-that-ended-in-a-mortality-outcome."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in ICD-10 long title), in the year 2015.": [[67, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-ICD-10-long-title),-in-the-year-2015."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in diagnosisstring), discharged in the year 2015.": [[64, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-diagnosisstring),-discharged-in-the-year-2015."]], "Example 2. Get measurements for all visits in or after 2020.": [[68, "Example-2.-Get-measurements-for-all-visits-in-or-after-2020."]], "Example 2a. How many sodium tests were placed between Apr 1, 2015 and May 31, 2015 at hospital 101?": [[65, "Example-2a.-How-many-sodium-tests-were-placed-between-Apr-1,-2015-and-May-31,-2015-at-hospital-101?"]], "Example 3. Advanced - uses ConditionRegexMatch from cycquery.ops. Get all patient encounters with diagnoses (ICD-9 long title contains schizophrenia and chronic ), in the year 2015.": [[67, "Example-3.-Advanced---uses-ConditionRegexMatch-from-cycquery.ops.-Get-all-patient-encounters-with-diagnoses-(ICD-9-long-title-contains-schizophrenia-and-chronic-),-in-the-year-2015."]], "Example 3. Get potassium lab tests for female patients.": [[66, "Example-3.-Get-potassium-lab-tests-for-female-patients."]], "Example 3. Get potassium lab tests for patients discharged in the year 2014, for all teaching hospitals.": [[64, "Example-3.-Get-potassium-lab-tests-for-patients-discharged-in-the-year-2014,-for-all-teaching-hospitals."]], "Example 4. Get AaDO2 carevue chart events for male patients that have a valuenum of less than 20.": [[66, "Example-4.-Get-AaDO2-carevue-chart-events-for-male-patients-that-have-a-valuenum-of-less-than-20."]], "Example 4. Get glucose medications (substring search) for female patients discharged in 2014.": [[64, "Example-4.-Get-glucose-medications-(substring-search)-for-female-patients-discharged-in-2014."]], "Example 4. Get routine vital signs for patients from year 2015.": [[67, "Example-4.-Get-routine-vital-signs-for-patients-from-year-2015."]], "Example 5. Get hemoglobin lab tests for patients from year 2009.": [[67, "Example-5.-Get-hemoglobin-lab-tests-for-patients-from-year-2009."]], "Example 6. Get radiology reports and filter on keywords lymphadenopathy and infectious occurring together from year 2009.": [[67, "Example-6.-Get-radiology-reports-and-filter-on-keywords-lymphadenopathy-and-infectious-occurring-together-from-year-2009."]], "Example 7. Get all female patient encounters from year 2015, and return batches partitioned and indexed on subject_id.": [[67, "Example-7.-Get-all-female-patient-encounters-from-year-2015,-and-return-batches-partitioned-and-indexed-on-subject_id."]], "Example 8. Running a raw SQL string.": [[67, "Example-8.-Running-a-raw-SQL-string."]], "GEMINI tutorial": [[65, "GEMINI-tutorial"]], "Imports and instantiate EICUQuerier": [[64, "Imports-and-instantiate-EICUQuerier"]], "Imports and instantiate GEMINIQuerier.": [[65, "Imports-and-instantiate-GEMINIQuerier."]], "Imports and instantiate MIMICIIIQuerier": [[66, "Imports-and-instantiate-MIMICIIIQuerier"]], "Imports and instantiate MIMICIVQuerier": [[67, "Imports-and-instantiate-MIMICIVQuerier"]], "Imports and instantiate OMOPQuerier.": [[68, "Imports-and-instantiate-OMOPQuerier."], [68, "id1"]], "Installing cycquery using pip": [[3, "installing-cycquery-using-pip"]], "MIMIC-III tutorial": [[66, "MIMIC-III-tutorial"]], "MIMIC-IV tutorial": [[67, "MIMIC-IV-tutorial"]], "OMOP tutorial": [[68, "OMOP-tutorial"]], "Pre-commit hooks": [[1, "pre-commit-hooks"]], "Query postgresql database": [[3, "query-postgresql-database"]], "Tutorials": [[63, "tutorials"]], "Using poetry": [[3, "using-poetry"]], "Welcome to cycquery\u2019s documentation!": [[2, "welcome-to-cycquery-s-documentation"]], "cycquery": [[3, "cycquery"], [62, "module-cycquery"]], "cycquery.base": [[4, "module-cycquery.base"]], "cycquery.base.DatasetQuerier": [[5, "cycquery-base-datasetquerier"]], "cycquery.eicu": [[6, "module-cycquery.eicu"]], "cycquery.eicu.EICUQuerier": [[7, "cycquery-eicu-eicuquerier"]], "cycquery.gemini": [[8, "module-cycquery.gemini"]], "cycquery.gemini.GEMINIQuerier": [[9, "cycquery-gemini-geminiquerier"]], "cycquery.interface": [[10, "module-cycquery.interface"]], "cycquery.interface.QueryInterface": [[11, "cycquery-interface-queryinterface"]], "cycquery.mimiciii": [[12, "module-cycquery.mimiciii"]], "cycquery.mimiciii.MIMICIIIQuerier": [[13, "cycquery-mimiciii-mimiciiiquerier"]], "cycquery.mimiciv": [[14, "module-cycquery.mimiciv"]], "cycquery.mimiciv.MIMICIVQuerier": [[15, "cycquery-mimiciv-mimicivquerier"]], "cycquery.omop": [[16, "module-cycquery.omop"]], "cycquery.omop.OMOPQuerier": [[17, "cycquery-omop-omopquerier"]], "cycquery.ops": [[18, "module-cycquery.ops"]], "cycquery.ops.AddColumn": [[19, "cycquery-ops-addcolumn"]], "cycquery.ops.AddDeltaColumn": [[20, "cycquery-ops-adddeltacolumn"]], "cycquery.ops.AddDeltaConstant": [[21, "cycquery-ops-adddeltaconstant"]], "cycquery.ops.AddNumeric": [[22, "cycquery-ops-addnumeric"]], "cycquery.ops.And": [[23, "cycquery-ops-and"]], "cycquery.ops.Apply": [[24, "cycquery-ops-apply"]], "cycquery.ops.Cast": [[25, "cycquery-ops-cast"]], "cycquery.ops.ConditionAfterDate": [[26, "cycquery-ops-conditionafterdate"]], "cycquery.ops.ConditionBeforeDate": [[27, "cycquery-ops-conditionbeforedate"]], "cycquery.ops.ConditionEndsWith": [[28, "cycquery-ops-conditionendswith"]], "cycquery.ops.ConditionEquals": [[29, "cycquery-ops-conditionequals"]], "cycquery.ops.ConditionGreaterThan": [[30, "cycquery-ops-conditiongreaterthan"]], "cycquery.ops.ConditionIn": [[31, "cycquery-ops-conditionin"]], "cycquery.ops.ConditionInMonths": [[32, "cycquery-ops-conditioninmonths"]], "cycquery.ops.ConditionInYears": [[33, "cycquery-ops-conditioninyears"]], "cycquery.ops.ConditionLessThan": [[34, "cycquery-ops-conditionlessthan"]], "cycquery.ops.ConditionLike": [[35, "cycquery-ops-conditionlike"]], "cycquery.ops.ConditionRegexMatch": [[36, "cycquery-ops-conditionregexmatch"]], "cycquery.ops.ConditionStartsWith": [[37, "cycquery-ops-conditionstartswith"]], "cycquery.ops.ConditionSubstring": [[38, "cycquery-ops-conditionsubstring"]], "cycquery.ops.Count": [[39, "cycquery-ops-count"]], "cycquery.ops.Distinct": [[40, "cycquery-ops-distinct"]], "cycquery.ops.Drop": [[41, "cycquery-ops-drop"]], "cycquery.ops.DropEmpty": [[42, "cycquery-ops-dropempty"]], "cycquery.ops.DropNulls": [[43, "cycquery-ops-dropnulls"]], "cycquery.ops.ExtractTimestampComponent": [[44, "cycquery-ops-extracttimestampcomponent"]], "cycquery.ops.FillNull": [[45, "cycquery-ops-fillnull"]], "cycquery.ops.GroupByAggregate": [[46, "cycquery-ops-groupbyaggregate"]], "cycquery.ops.Join": [[47, "cycquery-ops-join"]], "cycquery.ops.Keep": [[48, "cycquery-ops-keep"]], "cycquery.ops.Limit": [[49, "cycquery-ops-limit"]], "cycquery.ops.Literal": [[50, "cycquery-ops-literal"]], "cycquery.ops.Or": [[51, "cycquery-ops-or"]], "cycquery.ops.OrderBy": [[52, "cycquery-ops-orderby"]], "cycquery.ops.QueryOp": [[53, "cycquery-ops-queryop"]], "cycquery.ops.RandomizeOrder": [[54, "cycquery-ops-randomizeorder"]], "cycquery.ops.Rename": [[55, "cycquery-ops-rename"]], "cycquery.ops.Reorder": [[56, "cycquery-ops-reorder"]], "cycquery.ops.ReorderAfter": [[57, "cycquery-ops-reorderafter"]], "cycquery.ops.Sequential": [[58, "cycquery-ops-sequential"]], "cycquery.ops.Substring": [[59, "cycquery-ops-substring"]], "cycquery.ops.Trim": [[60, "cycquery-ops-trim"]], "cycquery.ops.Union": [[61, "cycquery-ops-union"]], "dataset APIs": [[62, "dataset-apis"]], "eICU-CRD tutorial": [[64, "eICU-CRD-tutorial"]], "\ud83d\udc23 Getting Started": [[3, "getting-started"]], "\ud83d\udcda Documentation": [[3, "documentation"]], "\ud83e\uddd1\ud83c\udfff\u200d\ud83d\udcbb Developing": [[3, "developing"]]}, "docnames": ["api", "contributing", "index", "intro", "reference/api/_autosummary/cycquery.base", "reference/api/_autosummary/cycquery.base.DatasetQuerier", "reference/api/_autosummary/cycquery.eicu", "reference/api/_autosummary/cycquery.eicu.EICUQuerier", "reference/api/_autosummary/cycquery.gemini", "reference/api/_autosummary/cycquery.gemini.GEMINIQuerier", "reference/api/_autosummary/cycquery.interface", "reference/api/_autosummary/cycquery.interface.QueryInterface", "reference/api/_autosummary/cycquery.mimiciii", "reference/api/_autosummary/cycquery.mimiciii.MIMICIIIQuerier", "reference/api/_autosummary/cycquery.mimiciv", "reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier", "reference/api/_autosummary/cycquery.omop", "reference/api/_autosummary/cycquery.omop.OMOPQuerier", "reference/api/_autosummary/cycquery.ops", "reference/api/_autosummary/cycquery.ops.AddColumn", "reference/api/_autosummary/cycquery.ops.AddDeltaColumn", "reference/api/_autosummary/cycquery.ops.AddDeltaConstant", "reference/api/_autosummary/cycquery.ops.AddNumeric", "reference/api/_autosummary/cycquery.ops.And", "reference/api/_autosummary/cycquery.ops.Apply", "reference/api/_autosummary/cycquery.ops.Cast", "reference/api/_autosummary/cycquery.ops.ConditionAfterDate", "reference/api/_autosummary/cycquery.ops.ConditionBeforeDate", "reference/api/_autosummary/cycquery.ops.ConditionEndsWith", "reference/api/_autosummary/cycquery.ops.ConditionEquals", "reference/api/_autosummary/cycquery.ops.ConditionGreaterThan", "reference/api/_autosummary/cycquery.ops.ConditionIn", "reference/api/_autosummary/cycquery.ops.ConditionInMonths", "reference/api/_autosummary/cycquery.ops.ConditionInYears", "reference/api/_autosummary/cycquery.ops.ConditionLessThan", "reference/api/_autosummary/cycquery.ops.ConditionLike", "reference/api/_autosummary/cycquery.ops.ConditionRegexMatch", "reference/api/_autosummary/cycquery.ops.ConditionStartsWith", "reference/api/_autosummary/cycquery.ops.ConditionSubstring", "reference/api/_autosummary/cycquery.ops.Count", "reference/api/_autosummary/cycquery.ops.Distinct", "reference/api/_autosummary/cycquery.ops.Drop", "reference/api/_autosummary/cycquery.ops.DropEmpty", "reference/api/_autosummary/cycquery.ops.DropNulls", "reference/api/_autosummary/cycquery.ops.ExtractTimestampComponent", "reference/api/_autosummary/cycquery.ops.FillNull", "reference/api/_autosummary/cycquery.ops.GroupByAggregate", "reference/api/_autosummary/cycquery.ops.Join", "reference/api/_autosummary/cycquery.ops.Keep", "reference/api/_autosummary/cycquery.ops.Limit", "reference/api/_autosummary/cycquery.ops.Literal", "reference/api/_autosummary/cycquery.ops.Or", "reference/api/_autosummary/cycquery.ops.OrderBy", "reference/api/_autosummary/cycquery.ops.QueryOp", "reference/api/_autosummary/cycquery.ops.RandomizeOrder", "reference/api/_autosummary/cycquery.ops.Rename", "reference/api/_autosummary/cycquery.ops.Reorder", "reference/api/_autosummary/cycquery.ops.ReorderAfter", "reference/api/_autosummary/cycquery.ops.Sequential", "reference/api/_autosummary/cycquery.ops.Substring", "reference/api/_autosummary/cycquery.ops.Trim", "reference/api/_autosummary/cycquery.ops.Union", "reference/api/cycquery", "tutorials", "tutorials/eicu", "tutorials/gemini", "tutorials/mimiciii", "tutorials/mimiciv", "tutorials/omop"], "envversion": {"nbsphinx": 4, "sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1}, "filenames": ["api.rst", "contributing.rst", "index.rst", "intro.rst", "reference/api/_autosummary/cycquery.base.rst", "reference/api/_autosummary/cycquery.base.DatasetQuerier.rst", "reference/api/_autosummary/cycquery.eicu.rst", "reference/api/_autosummary/cycquery.eicu.EICUQuerier.rst", "reference/api/_autosummary/cycquery.gemini.rst", "reference/api/_autosummary/cycquery.gemini.GEMINIQuerier.rst", "reference/api/_autosummary/cycquery.interface.rst", "reference/api/_autosummary/cycquery.interface.QueryInterface.rst", "reference/api/_autosummary/cycquery.mimiciii.rst", "reference/api/_autosummary/cycquery.mimiciii.MIMICIIIQuerier.rst", "reference/api/_autosummary/cycquery.mimiciv.rst", "reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.rst", "reference/api/_autosummary/cycquery.omop.rst", "reference/api/_autosummary/cycquery.omop.OMOPQuerier.rst", "reference/api/_autosummary/cycquery.ops.rst", "reference/api/_autosummary/cycquery.ops.AddColumn.rst", "reference/api/_autosummary/cycquery.ops.AddDeltaColumn.rst", "reference/api/_autosummary/cycquery.ops.AddDeltaConstant.rst", "reference/api/_autosummary/cycquery.ops.AddNumeric.rst", "reference/api/_autosummary/cycquery.ops.And.rst", "reference/api/_autosummary/cycquery.ops.Apply.rst", "reference/api/_autosummary/cycquery.ops.Cast.rst", "reference/api/_autosummary/cycquery.ops.ConditionAfterDate.rst", "reference/api/_autosummary/cycquery.ops.ConditionBeforeDate.rst", "reference/api/_autosummary/cycquery.ops.ConditionEndsWith.rst", "reference/api/_autosummary/cycquery.ops.ConditionEquals.rst", "reference/api/_autosummary/cycquery.ops.ConditionGreaterThan.rst", "reference/api/_autosummary/cycquery.ops.ConditionIn.rst", "reference/api/_autosummary/cycquery.ops.ConditionInMonths.rst", "reference/api/_autosummary/cycquery.ops.ConditionInYears.rst", "reference/api/_autosummary/cycquery.ops.ConditionLessThan.rst", "reference/api/_autosummary/cycquery.ops.ConditionLike.rst", "reference/api/_autosummary/cycquery.ops.ConditionRegexMatch.rst", "reference/api/_autosummary/cycquery.ops.ConditionStartsWith.rst", "reference/api/_autosummary/cycquery.ops.ConditionSubstring.rst", "reference/api/_autosummary/cycquery.ops.Count.rst", "reference/api/_autosummary/cycquery.ops.Distinct.rst", "reference/api/_autosummary/cycquery.ops.Drop.rst", "reference/api/_autosummary/cycquery.ops.DropEmpty.rst", "reference/api/_autosummary/cycquery.ops.DropNulls.rst", "reference/api/_autosummary/cycquery.ops.ExtractTimestampComponent.rst", "reference/api/_autosummary/cycquery.ops.FillNull.rst", "reference/api/_autosummary/cycquery.ops.GroupByAggregate.rst", "reference/api/_autosummary/cycquery.ops.Join.rst", "reference/api/_autosummary/cycquery.ops.Keep.rst", "reference/api/_autosummary/cycquery.ops.Limit.rst", "reference/api/_autosummary/cycquery.ops.Literal.rst", "reference/api/_autosummary/cycquery.ops.Or.rst", "reference/api/_autosummary/cycquery.ops.OrderBy.rst", "reference/api/_autosummary/cycquery.ops.QueryOp.rst", "reference/api/_autosummary/cycquery.ops.RandomizeOrder.rst", "reference/api/_autosummary/cycquery.ops.Rename.rst", "reference/api/_autosummary/cycquery.ops.Reorder.rst", "reference/api/_autosummary/cycquery.ops.ReorderAfter.rst", "reference/api/_autosummary/cycquery.ops.Sequential.rst", "reference/api/_autosummary/cycquery.ops.Substring.rst", "reference/api/_autosummary/cycquery.ops.Trim.rst", "reference/api/_autosummary/cycquery.ops.Union.rst", "reference/api/cycquery.rst", "tutorials.rst", "tutorials/eicu.ipynb", "tutorials/gemini.ipynb", "tutorials/mimiciii.ipynb", "tutorials/mimiciv.ipynb", "tutorials/omop.ipynb"], "indexentries": {"__add__() (sequential method)": [[58, "cycquery.ops.Sequential.__add__", false]], "__call__() (addcolumn method)": [[19, "cycquery.ops.AddColumn.__call__", false]], "__call__() (adddeltacolumn method)": [[20, "cycquery.ops.AddDeltaColumn.__call__", false]], "__call__() (adddeltaconstant method)": [[21, "cycquery.ops.AddDeltaConstant.__call__", false]], "__call__() (addnumeric method)": [[22, "cycquery.ops.AddNumeric.__call__", false]], "__call__() (and method)": [[23, "cycquery.ops.And.__call__", false]], "__call__() (apply method)": [[24, "cycquery.ops.Apply.__call__", false]], "__call__() (cast method)": [[25, "cycquery.ops.Cast.__call__", false]], "__call__() (conditionafterdate method)": [[26, "cycquery.ops.ConditionAfterDate.__call__", false]], "__call__() (conditionbeforedate method)": [[27, "cycquery.ops.ConditionBeforeDate.__call__", false]], "__call__() (conditionendswith method)": [[28, "cycquery.ops.ConditionEndsWith.__call__", false]], "__call__() (conditionequals method)": [[29, "cycquery.ops.ConditionEquals.__call__", false]], "__call__() (conditiongreaterthan method)": [[30, "cycquery.ops.ConditionGreaterThan.__call__", false]], "__call__() (conditionin method)": [[31, "cycquery.ops.ConditionIn.__call__", false]], "__call__() (conditioninmonths method)": [[32, "cycquery.ops.ConditionInMonths.__call__", false]], "__call__() (conditioninyears method)": [[33, "cycquery.ops.ConditionInYears.__call__", false]], "__call__() (conditionlessthan method)": [[34, "cycquery.ops.ConditionLessThan.__call__", false]], "__call__() (conditionlike method)": [[35, "cycquery.ops.ConditionLike.__call__", false]], "__call__() (conditionregexmatch method)": [[36, "cycquery.ops.ConditionRegexMatch.__call__", false]], "__call__() (conditionstartswith method)": [[37, "cycquery.ops.ConditionStartsWith.__call__", false]], "__call__() (conditionsubstring method)": [[38, "cycquery.ops.ConditionSubstring.__call__", false]], "__call__() (count method)": [[39, "cycquery.ops.Count.__call__", false]], "__call__() (distinct method)": [[40, "cycquery.ops.Distinct.__call__", false]], "__call__() (drop method)": [[41, "cycquery.ops.Drop.__call__", false]], "__call__() (dropempty method)": [[42, "cycquery.ops.DropEmpty.__call__", false]], "__call__() (dropnulls method)": [[43, "cycquery.ops.DropNulls.__call__", false]], "__call__() (extracttimestampcomponent method)": [[44, "cycquery.ops.ExtractTimestampComponent.__call__", false]], "__call__() (fillnull method)": [[45, "cycquery.ops.FillNull.__call__", false]], "__call__() (groupbyaggregate method)": [[46, "cycquery.ops.GroupByAggregate.__call__", false]], "__call__() (join method)": [[47, "cycquery.ops.Join.__call__", false]], "__call__() (keep method)": [[48, "cycquery.ops.Keep.__call__", false]], "__call__() (limit method)": [[49, "cycquery.ops.Limit.__call__", false]], "__call__() (literal method)": [[50, "cycquery.ops.Literal.__call__", false]], "__call__() (or method)": [[51, "cycquery.ops.Or.__call__", false]], "__call__() (orderby method)": [[52, "cycquery.ops.OrderBy.__call__", false]], "__call__() (queryop method)": [[53, "cycquery.ops.QueryOp.__call__", false]], "__call__() (randomizeorder method)": [[54, "cycquery.ops.RandomizeOrder.__call__", false]], "__call__() (rename method)": [[55, "cycquery.ops.Rename.__call__", false]], "__call__() (reorder method)": [[56, "cycquery.ops.Reorder.__call__", false]], "__call__() (reorderafter method)": [[57, "cycquery.ops.ReorderAfter.__call__", false]], "__call__() (sequential method)": [[58, "cycquery.ops.Sequential.__call__", false]], "__call__() (substring method)": [[59, "cycquery.ops.Substring.__call__", false]], "__call__() (trim method)": [[60, "cycquery.ops.Trim.__call__", false]], "__call__() (union method)": [[61, "cycquery.ops.Union.__call__", false]], "__init__() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.__init__", false]], "__init__() (sequential method)": [[58, "cycquery.ops.Sequential.__init__", false]], "addcolumn (class in cycquery.ops)": [[19, "cycquery.ops.AddColumn", false]], "adddeltacolumn (class in cycquery.ops)": [[20, "cycquery.ops.AddDeltaColumn", false]], "adddeltaconstant (class in cycquery.ops)": [[21, "cycquery.ops.AddDeltaConstant", false]], "addnumeric (class in cycquery.ops)": [[22, "cycquery.ops.AddNumeric", false]], "and (class in cycquery.ops)": [[23, "cycquery.ops.And", false]], "append() (sequential method)": [[58, "cycquery.ops.Sequential.append", false]], "apply (class in cycquery.ops)": [[24, "cycquery.ops.Apply", false]], "care_units() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.care_units", false]], "cast (class in cycquery.ops)": [[25, "cycquery.ops.Cast", false]], "chartevents() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.chartevents", false]], "chartevents() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.chartevents", false]], "clear_data() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.clear_data", false]], "conditionafterdate (class in cycquery.ops)": [[26, "cycquery.ops.ConditionAfterDate", false]], "conditionbeforedate (class in cycquery.ops)": [[27, "cycquery.ops.ConditionBeforeDate", false]], "conditionendswith (class in cycquery.ops)": [[28, "cycquery.ops.ConditionEndsWith", false]], "conditionequals (class in cycquery.ops)": [[29, "cycquery.ops.ConditionEquals", false]], "conditiongreaterthan (class in cycquery.ops)": [[30, "cycquery.ops.ConditionGreaterThan", false]], "conditionin (class in cycquery.ops)": [[31, "cycquery.ops.ConditionIn", false]], "conditioninmonths (class in cycquery.ops)": [[32, "cycquery.ops.ConditionInMonths", false]], "conditioninyears (class in cycquery.ops)": [[33, "cycquery.ops.ConditionInYears", false]], "conditionlessthan (class in cycquery.ops)": [[34, "cycquery.ops.ConditionLessThan", false]], "conditionlike (class in cycquery.ops)": [[35, "cycquery.ops.ConditionLike", false]], "conditionregexmatch (class in cycquery.ops)": [[36, "cycquery.ops.ConditionRegexMatch", false]], "conditionstartswith (class in cycquery.ops)": [[37, "cycquery.ops.ConditionStartsWith", false]], "conditionsubstring (class in cycquery.ops)": [[38, "cycquery.ops.ConditionSubstring", false]], "count (class in cycquery.ops)": [[39, "cycquery.ops.Count", false]], "cycquery": [[62, "module-cycquery", false]], "cycquery.base": [[4, "module-cycquery.base", false]], "cycquery.eicu": [[6, "module-cycquery.eicu", false]], "cycquery.gemini": [[8, "module-cycquery.gemini", false]], "cycquery.interface": [[10, "module-cycquery.interface", false]], "cycquery.mimiciii": [[12, "module-cycquery.mimiciii", false]], "cycquery.mimiciv": [[14, "module-cycquery.mimiciv", false]], "cycquery.omop": [[16, "module-cycquery.omop", false]], "cycquery.ops": [[18, "module-cycquery.ops", false]], "data (queryinterface property)": [[11, "cycquery.interface.QueryInterface.data", false]], "datasetquerier (class in cycquery.base)": [[5, "cycquery.base.DatasetQuerier", false]], "db (datasetquerier attribute)": [[5, "cycquery.base.DatasetQuerier.db", false]], "diagnoses() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.diagnoses", false]], "diagnoses() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.diagnoses", false]], "diagnoses_icd() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.diagnoses_icd", false]], "distinct (class in cycquery.ops)": [[40, "cycquery.ops.Distinct", false]], "drop (class in cycquery.ops)": [[41, "cycquery.ops.Drop", false]], "dropempty (class in cycquery.ops)": [[42, "cycquery.ops.DropEmpty", false]], "dropnulls (class in cycquery.ops)": [[43, "cycquery.ops.DropNulls", false]], "eicuquerier (class in cycquery.eicu)": [[7, "cycquery.eicu.EICUQuerier", false]], "extend() (sequential method)": [[58, "cycquery.ops.Sequential.extend", false]], "extracttimestampcomponent (class in cycquery.ops)": [[44, "cycquery.ops.ExtractTimestampComponent", false]], "fillnull (class in cycquery.ops)": [[45, "cycquery.ops.FillNull", false]], "geminiquerier (class in cycquery.gemini)": [[9, "cycquery.gemini.GEMINIQuerier", false]], "get_table() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.get_table", false]], "get_table() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.get_table", false]], "get_table() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.get_table", false]], "get_table() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.get_table", false]], "get_table() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.get_table", false]], "get_table() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.get_table", false]], "groupbyaggregate (class in cycquery.ops)": [[46, "cycquery.ops.GroupByAggregate", false]], "imaging() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.imaging", false]], "insert() (sequential method)": [[58, "cycquery.ops.Sequential.insert", false]], "ip_admin() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.ip_admin", false]], "join (class in cycquery.ops)": [[47, "cycquery.ops.Join", false]], "join() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.join", false]], "keep (class in cycquery.ops)": [[48, "cycquery.ops.Keep", false]], "labevents() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.labevents", false]], "labevents() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.labevents", false]], "limit (class in cycquery.ops)": [[49, "cycquery.ops.Limit", false]], "list_columns() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_columns", false]], "list_columns() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_columns", false]], "list_columns() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_columns", false]], "list_columns() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_columns", false]], "list_columns() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_columns", false]], "list_columns() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_columns", false]], "list_custom_tables() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_custom_tables", false]], "list_custom_tables() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_custom_tables", false]], "list_custom_tables() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_custom_tables", false]], "list_custom_tables() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_custom_tables", false]], "list_custom_tables() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_custom_tables", false]], "list_custom_tables() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_custom_tables", false]], "list_schemas() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_schemas", false]], "list_schemas() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_schemas", false]], "list_schemas() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_schemas", false]], "list_schemas() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_schemas", false]], "list_schemas() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_schemas", false]], "list_schemas() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_schemas", false]], "list_tables() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_tables", false]], "list_tables() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_tables", false]], "list_tables() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_tables", false]], "list_tables() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_tables", false]], "list_tables() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_tables", false]], "list_tables() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_tables", false]], "literal (class in cycquery.ops)": [[50, "cycquery.ops.Literal", false]], "map_concept_ids_to_name() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.map_concept_ids_to_name", false]], "measurement() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.measurement", false]], "mimiciiiquerier (class in cycquery.mimiciii)": [[13, "cycquery.mimiciii.MIMICIIIQuerier", false]], "mimicivquerier (class in cycquery.mimiciv)": [[15, "cycquery.mimiciv.MIMICIVQuerier", false]], "module": [[4, "module-cycquery.base", false], [6, "module-cycquery.eicu", false], [8, "module-cycquery.gemini", false], [10, "module-cycquery.interface", false], [12, "module-cycquery.mimiciii", false], [14, "module-cycquery.mimiciv", false], [16, "module-cycquery.omop", false], [18, "module-cycquery.ops", false], [62, "module-cycquery", false]], "observation() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.observation", false]], "omopquerier (class in cycquery.omop)": [[17, "cycquery.omop.OMOPQuerier", false]], "ops() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.ops", false]], "or (class in cycquery.ops)": [[51, "cycquery.ops.Or", false]], "orderby (class in cycquery.ops)": [[52, "cycquery.ops.OrderBy", false]], "patients() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.patients", false]], "person() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.person", false]], "pop() (sequential method)": [[58, "cycquery.ops.Sequential.pop", false]], "procedures_icd() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.procedures_icd", false]], "queryinterface (class in cycquery.interface)": [[11, "cycquery.interface.QueryInterface", false]], "queryop (class in cycquery.ops)": [[53, "cycquery.ops.QueryOp", false]], "randomizeorder (class in cycquery.ops)": [[54, "cycquery.ops.RandomizeOrder", false]], "rename (class in cycquery.ops)": [[55, "cycquery.ops.Rename", false]], "reorder (class in cycquery.ops)": [[56, "cycquery.ops.Reorder", false]], "reorderafter (class in cycquery.ops)": [[57, "cycquery.ops.ReorderAfter", false]], "room_transfer() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.room_transfer", false]], "run() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.run", false]], "save() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.save", false]], "sequential (class in cycquery.ops)": [[58, "cycquery.ops.Sequential", false]], "substring (class in cycquery.ops)": [[59, "cycquery.ops.Substring", false]], "trim (class in cycquery.ops)": [[60, "cycquery.ops.Trim", false]], "union (class in cycquery.ops)": [[61, "cycquery.ops.Union", false]], "union() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.union", false]], "union_all() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.union_all", false]], "visit_detail() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.visit_detail", false]], "visit_occurrence() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.visit_occurrence", false]]}, "objects": {"": [[62, 0, 0, "-", "cycquery"]], "cycquery": [[4, 0, 0, "-", "base"], [6, 0, 0, "-", "eicu"], [8, 0, 0, "-", "gemini"], [10, 0, 0, "-", "interface"], [12, 0, 0, "-", "mimiciii"], [14, 0, 0, "-", "mimiciv"], [16, 0, 0, "-", "omop"], [18, 0, 0, "-", "ops"]], "cycquery.base": [[5, 1, 1, "", "DatasetQuerier"]], "cycquery.base.DatasetQuerier": [[5, 2, 1, "", "db"], [5, 3, 1, "", "get_table"], [5, 3, 1, "", "list_columns"], [5, 3, 1, "", "list_custom_tables"], [5, 3, 1, "", "list_schemas"], [5, 3, 1, "", "list_tables"]], "cycquery.eicu": [[7, 1, 1, "", "EICUQuerier"]], "cycquery.eicu.EICUQuerier": [[7, 3, 1, "", "get_table"], [7, 3, 1, "", "list_columns"], [7, 3, 1, "", "list_custom_tables"], [7, 3, 1, "", "list_schemas"], [7, 3, 1, "", "list_tables"]], "cycquery.gemini": [[9, 1, 1, "", "GEMINIQuerier"]], "cycquery.gemini.GEMINIQuerier": [[9, 3, 1, "", "care_units"], [9, 3, 1, "", "diagnoses"], [9, 3, 1, "", "get_table"], [9, 3, 1, "", "imaging"], [9, 3, 1, "", "ip_admin"], [9, 3, 1, "", "list_columns"], [9, 3, 1, "", "list_custom_tables"], [9, 3, 1, "", "list_schemas"], [9, 3, 1, "", "list_tables"], [9, 3, 1, "", "room_transfer"]], "cycquery.interface": [[11, 1, 1, "", "QueryInterface"]], "cycquery.interface.QueryInterface": [[11, 3, 1, "", "__init__"], [11, 3, 1, "", "clear_data"], [11, 4, 1, "", "data"], [11, 3, 1, "", "join"], [11, 3, 1, "", "ops"], [11, 3, 1, "", "run"], [11, 3, 1, "", "save"], [11, 3, 1, "", "union"], [11, 3, 1, "", "union_all"]], "cycquery.mimiciii": [[13, 1, 1, "", "MIMICIIIQuerier"]], "cycquery.mimiciii.MIMICIIIQuerier": [[13, 3, 1, "", "chartevents"], [13, 3, 1, "", "diagnoses"], [13, 3, 1, "", "get_table"], [13, 3, 1, "", "labevents"], [13, 3, 1, "", "list_columns"], [13, 3, 1, "", "list_custom_tables"], [13, 3, 1, "", "list_schemas"], [13, 3, 1, "", "list_tables"]], "cycquery.mimiciv": [[15, 1, 1, "", "MIMICIVQuerier"]], "cycquery.mimiciv.MIMICIVQuerier": [[15, 3, 1, "", "chartevents"], [15, 3, 1, "", "diagnoses_icd"], [15, 3, 1, "", "get_table"], [15, 3, 1, "", "labevents"], [15, 3, 1, "", "list_columns"], [15, 3, 1, "", "list_custom_tables"], [15, 3, 1, "", "list_schemas"], [15, 3, 1, "", "list_tables"], [15, 3, 1, "", "patients"], [15, 3, 1, "", "procedures_icd"]], "cycquery.omop": [[17, 1, 1, "", "OMOPQuerier"]], "cycquery.omop.OMOPQuerier": [[17, 3, 1, "", "get_table"], [17, 3, 1, "", "list_columns"], [17, 3, 1, "", "list_custom_tables"], [17, 3, 1, "", "list_schemas"], [17, 3, 1, "", "list_tables"], [17, 3, 1, "", "map_concept_ids_to_name"], [17, 3, 1, "", "measurement"], [17, 3, 1, "", "observation"], [17, 3, 1, "", "person"], [17, 3, 1, "", "visit_detail"], [17, 3, 1, "", "visit_occurrence"]], "cycquery.ops": [[19, 1, 1, "", "AddColumn"], [20, 1, 1, "", "AddDeltaColumn"], [21, 1, 1, "", "AddDeltaConstant"], [22, 1, 1, "", "AddNumeric"], [23, 1, 1, "", "And"], [24, 1, 1, "", "Apply"], [25, 1, 1, "", "Cast"], [26, 1, 1, "", "ConditionAfterDate"], [27, 1, 1, "", "ConditionBeforeDate"], [28, 1, 1, "", "ConditionEndsWith"], [29, 1, 1, "", "ConditionEquals"], [30, 1, 1, "", "ConditionGreaterThan"], [31, 1, 1, "", "ConditionIn"], [32, 1, 1, "", "ConditionInMonths"], [33, 1, 1, "", "ConditionInYears"], [34, 1, 1, "", "ConditionLessThan"], [35, 1, 1, "", "ConditionLike"], [36, 1, 1, "", "ConditionRegexMatch"], [37, 1, 1, "", "ConditionStartsWith"], [38, 1, 1, "", "ConditionSubstring"], [39, 1, 1, "", "Count"], [40, 1, 1, "", "Distinct"], [41, 1, 1, "", "Drop"], [42, 1, 1, "", "DropEmpty"], [43, 1, 1, "", "DropNulls"], [44, 1, 1, "", "ExtractTimestampComponent"], [45, 1, 1, "", "FillNull"], [46, 1, 1, "", "GroupByAggregate"], [47, 1, 1, "", "Join"], [48, 1, 1, "", "Keep"], [49, 1, 1, "", "Limit"], [50, 1, 1, "", "Literal"], [51, 1, 1, "", "Or"], [52, 1, 1, "", "OrderBy"], [53, 1, 1, "", "QueryOp"], [54, 1, 1, "", "RandomizeOrder"], [55, 1, 1, "", "Rename"], [56, 1, 1, "", "Reorder"], [57, 1, 1, "", "ReorderAfter"], [58, 1, 1, "", "Sequential"], [59, 1, 1, "", "Substring"], [60, 1, 1, "", "Trim"], [61, 1, 1, "", "Union"]], "cycquery.ops.AddColumn": [[19, 3, 1, "", "__call__"]], "cycquery.ops.AddDeltaColumn": [[20, 3, 1, "", "__call__"]], "cycquery.ops.AddDeltaConstant": [[21, 3, 1, "", "__call__"]], "cycquery.ops.AddNumeric": [[22, 3, 1, "", "__call__"]], "cycquery.ops.And": [[23, 3, 1, "", "__call__"]], "cycquery.ops.Apply": [[24, 3, 1, "", "__call__"]], "cycquery.ops.Cast": [[25, 3, 1, "", "__call__"]], "cycquery.ops.ConditionAfterDate": [[26, 3, 1, "", "__call__"]], "cycquery.ops.ConditionBeforeDate": [[27, 3, 1, "", "__call__"]], "cycquery.ops.ConditionEndsWith": [[28, 3, 1, "", "__call__"]], "cycquery.ops.ConditionEquals": [[29, 3, 1, "", "__call__"]], "cycquery.ops.ConditionGreaterThan": [[30, 3, 1, "", "__call__"]], "cycquery.ops.ConditionIn": [[31, 3, 1, "", "__call__"]], "cycquery.ops.ConditionInMonths": [[32, 3, 1, "", "__call__"]], "cycquery.ops.ConditionInYears": [[33, 3, 1, "", "__call__"]], "cycquery.ops.ConditionLessThan": [[34, 3, 1, "", "__call__"]], "cycquery.ops.ConditionLike": [[35, 3, 1, "", "__call__"]], "cycquery.ops.ConditionRegexMatch": [[36, 3, 1, "", "__call__"]], "cycquery.ops.ConditionStartsWith": [[37, 3, 1, "", "__call__"]], "cycquery.ops.ConditionSubstring": [[38, 3, 1, "", "__call__"]], "cycquery.ops.Count": [[39, 3, 1, "", "__call__"]], "cycquery.ops.Distinct": [[40, 3, 1, "", "__call__"]], "cycquery.ops.Drop": [[41, 3, 1, "", "__call__"]], "cycquery.ops.DropEmpty": [[42, 3, 1, "", "__call__"]], "cycquery.ops.DropNulls": [[43, 3, 1, "", "__call__"]], "cycquery.ops.ExtractTimestampComponent": [[44, 3, 1, "", "__call__"]], "cycquery.ops.FillNull": [[45, 3, 1, "", "__call__"]], "cycquery.ops.GroupByAggregate": [[46, 3, 1, "", "__call__"]], "cycquery.ops.Join": [[47, 3, 1, "", "__call__"]], "cycquery.ops.Keep": [[48, 3, 1, "", "__call__"]], "cycquery.ops.Limit": [[49, 3, 1, "", "__call__"]], "cycquery.ops.Literal": [[50, 3, 1, "", "__call__"]], "cycquery.ops.Or": [[51, 3, 1, "", "__call__"]], "cycquery.ops.OrderBy": [[52, 3, 1, "", "__call__"]], "cycquery.ops.QueryOp": [[53, 3, 1, "", "__call__"]], "cycquery.ops.RandomizeOrder": [[54, 3, 1, "", "__call__"]], "cycquery.ops.Rename": [[55, 3, 1, "", "__call__"]], "cycquery.ops.Reorder": [[56, 3, 1, "", "__call__"]], "cycquery.ops.ReorderAfter": [[57, 3, 1, "", "__call__"]], "cycquery.ops.Sequential": [[58, 3, 1, "", "__add__"], [58, 3, 1, "", "__call__"], [58, 3, 1, "", "__init__"], [58, 3, 1, "", "append"], [58, 3, 1, "", "extend"], [58, 3, 1, "", "insert"], [58, 3, 1, "", "pop"]], "cycquery.ops.Substring": [[59, 3, 1, "", "__call__"]], "cycquery.ops.Trim": [[60, 3, 1, "", "__call__"]], "cycquery.ops.Union": [[61, 3, 1, "", "__call__"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "attribute", "Python attribute"], "3": ["py", "method", "Python method"], "4": ["py", "property", "Python property"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:attribute", "3": "py:method", "4": "py:property"}, "terms": {"": [5, 11, 17, 24, 45, 64, 65, 66, 67, 68], "0": [14, 45, 59, 64, 65, 66, 67, 68], "00": [67, 68], "003948": 67, "01": [26, 27, 65, 67, 68], "013149": 67, "013243": 67, "02": 68, "03": 65, "04": [65, 68], "05": 65, "06": [67, 68], "07": [64, 66, 67], "08": [67, 68], "09": [64, 65, 66, 67, 68], "093352": 65, "094": 67, "095": 67, "1": [3, 11, 21, 22, 24, 26, 27, 29, 30, 31, 32, 34, 45, 50, 63], "10": [49, 63, 68], "100": [63, 66, 67, 68], "1000": 67, "1000000": 11, "101": 63, "101793": 64, "107843": 67, "11": [64, 68], "12": 64, "130": 67, "132": 67, "14": 67, "142": 67, "145693": 65, "15": [64, 67, 68], "160325": 67, "169": 67, "17": [64, 65, 66, 67, 68], "170": [67, 68], "171": 68, "180899": 66, "183889": 64, "189734": 65, "19": [65, 67], "1a": 63, "1b": 63, "1c": 63, "2": [3, 14, 22, 24, 31, 32, 59, 63, 65], "20": 63, "2009": 63, "2010": 63, "2011": 68, "2012": 68, "2013": 68, "2014": [63, 68], "2015": [63, 68], "2016": [63, 68], "2017": 68, "2018": 68, "2019": [33, 68], "2020": [26, 27, 33, 63], "2021": [63, 68], "2022": 68, "2023": [65, 68], "2024": [64, 66, 67, 68], "21": [64, 65], "234838": 66, "243": 67, "245": 67, "26": 65, "271": 68, "271381": 68, "271455": 68, "289": 66, "294": 68, "2a": 63, "3": [63, 65, 68], "306": 66, "308": 66, "31": 63, "32567": 65, "330425": 66, "34": 66, "35": 66, "369": 64, "371": 64, "39": [64, 65, 66, 67, 68], "4": [63, 65, 68], "407262": 64, "41": [64, 66, 67], "42": 67, "426": 68, "44": 66, "449": 65, "45": [65, 66], "47": 67, "477935": 67, "48": 68, "483853": 64, "490825": 68, "5": [63, 64, 65, 66, 68], "50": 67, "506": 65, "508": 67, "51": [65, 68], "510": 67, "514": 67, "52": 65, "53": 68, "54": 68, "5432": [3, 17, 64, 66, 67, 68], "564382": 66, "57": [66, 67], "574": 67, "577": 67, "58": 67, "5815": 68, "591": 65, "592": 65, "6": [63, 64, 65, 66, 68], "641": 66, "642": 66, "661": 68, "663": 68, "672": 68, "672677": 67, "674": 68, "675141": 65, "7": [63, 65, 68], "710405": 67, "776": 68, "779": 68, "8": [63, 68], "814": 65, "815": 65, "82": 67, "821": 64, "823": 64, "843": 67, "845": 67, "856": [64, 65], "857": 65, "857821": 68, "858": 64, "9": 63, "900": 64, "902": 65, "903": 65, "912": 67, "914": 67, "927": 66, "929": 66, "9305": 65, "936": 66, "938": 66, "939296": 65, "949": 66, "962": 64, "964": 64, "999": 67, "A": [10, 11, 21, 26, 27, 47], "And": [0, 67], "For": [1, 17], "If": [1, 17, 19, 20, 21, 22, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 52, 60], "In": 3, "It": [3, 24, 63], "No": [11, 68], "Not": 5, "OR": 51, "Or": 0, "The": [1, 3, 5, 11, 15, 20, 24, 48, 62, 63, 64, 66, 67, 68], "To": 1, "__add__": [0, 58], "__call__": [0, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "__init__": [0, 11, 58], "aado2": 63, "abov": 63, "abstract": 53, "accord": [17, 64, 66, 67, 68], "accordingli": [64, 66, 67, 68], "activ": 3, "ad": [11, 19, 20, 21, 22, 58], "add": [19, 20, 21, 22, 50, 58], "add_to": [19, 20, 21, 22], "addcolumn": 0, "adddeltacolumn": [0, 67], "adddeltaconst": 0, "addnumer": 0, "address": 5, "adjust": 15, "admdad": 65, "admiss": [63, 66], "admissiondrug": 64, "admissiondx": 64, "admittim": 67, "admitting_concept_id": 68, "advanc": 63, "after": [5, 15, 24, 26, 57, 58, 63], "aggfunc": 46, "aggreg": [3, 46], "aggsep": 46, "all": [1, 3, 11, 38, 52, 55, 61, 63, 65], "all_visit": 68, "allergi": 64, "allow": [5, 7, 9, 13, 15, 17, 63], "along": 1, "also": 24, "an": [1, 9, 11, 13, 15, 17, 20, 23, 47, 51, 55], "analysi": 1, "analyz": 54, "anchor_year": 15, "anchor_year_differ": 67, "anchor_year_group": 15, "ani": [11, 20, 28, 29, 30, 31, 34, 37, 38, 45, 50], "anoth": [11, 47, 55, 58], "any_": 38, "apacheapsvar": 64, "apachepatientresult": 64, "apachepredvar": 64, "api": [2, 3, 5, 7, 9, 13, 15, 16, 17, 63], "append": [0, 58], "appli": [0, 1, 15, 19, 20, 21, 22, 60], "approx": 63, "approxim": 15, "apr": 63, "april": 63, "ar": [5, 15, 24, 47], "arg": [53, 54, 58], "argument": [20, 28, 29, 30, 31, 34, 37, 38], "around": [3, 63], "ascend": [52, 65], "assign": 17, "assign_all_visit_id": 68, "assum": [24, 64, 66, 67, 68], "attent": 19, "attribut": 11, "automat": 5, "b": 38, "backend": 11, "base": [0, 3, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "batch": [11, 63], "batch_mod": [11, 67], "batch_siz": [11, 67], "becom": [11, 54], "befor": [1, 27, 47], "being": [19, 20, 21, 22, 26, 27, 29, 32, 33], "between": 63, "bin": 3, "binarize_col": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "binaryexpress": [11, 47], "black": 1, "bodi": 68, "bool": [5, 7, 9, 11, 13, 15, 17, 19, 20, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 52, 55, 61], "boolean": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "both": 47, "build": [5, 63], "built": 3, "ca": 65, "call": 53, "callabl": 24, "can": [1, 3, 5, 7, 9, 13, 15, 17, 24, 38], "cannot": 54, "care": [9, 15], "care_sit": 68, "care_unit": [0, 9], "careplancareprovid": 64, "careplaneol": 64, "careplangener": 64, "careplango": 64, "careplaninfectiousdiseas": 64, "carevu": 63, "cartesian": 47, "cast": [0, 5, 7, 9, 11, 13, 15, 17, 65, 67], "cast_timestamp_col": [5, 7, 9, 13, 15, 17], "categori": 67, "cd": 3, "cdm_sourc": 68, "cdm_synthea10": 68, "certain": 54, "chain": [11, 58], "chart": [15, 63], "chart_ev": [66, 67], "chartev": [0, 13, 15, 66, 67], "chartevents_op": 66, "check": [1, 55], "check_exist": 55, "chronic": 63, "class": [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62], "clear": 11, "clear_data": [0, 11], "code": [2, 64, 66, 67, 68], "codestyl": 3, "cohort": 68, "cohort_definit": 68, "col": [19, 24, 25, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 48, 50, 52, 56, 57, 59, 60], "col1": [3, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 41, 42, 43, 44, 45, 47, 48, 50, 52, 55, 56, 57, 58, 59, 60], "col1_bool": [26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38], "col1_new": [24, 45, 55], "col1_plus_1": [21, 22], "col1_plus_col2": [19, 20], "col1_plus_col3": 19, "col1_substr": 59, "col1_trim": 60, "col2": [3, 19, 20, 21, 22, 24, 25, 41, 42, 43, 45, 47, 48, 52, 56, 57, 58, 60], "col2_new": [24, 45], "col2_plus_1": 22, "col2_plus_col3": 19, "col2_trim": 60, "col3": [3, 19, 20, 47, 57], "collection_date_tim": 65, "column": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 52, 55, 56, 57, 59, 60], "combin": [19, 23, 51], "come": 57, "commit": 2, "common": 68, "commun": 63, "complet": 56, "compon": 44, "comput": 11, "concept": [17, 68], "concept_ancestor": 68, "concept_class": 68, "concept_relationship": 68, "concept_synonym": 68, "cond": [11, 47], "cond_kwarg": [28, 29, 30, 31, 34, 37, 38], "cond_op": [23, 51], "condit": [3, 11, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 68], "condition_concept_id": 68, "condition_concept_nam": 68, "condition_era": 68, "condition_occurr": 68, "conditionafterd": [0, 65, 67, 68], "conditionbefored": [0, 65], "conditionendswith": 0, "conditionequ": [0, 64, 65, 66, 67], "conditiongreaterthan": 0, "conditionin": [0, 3, 23, 51], "conditioninmonth": 0, "conditioninyear": [0, 67], "conditionlessthan": [0, 66], "conditionlik": [0, 23, 51, 67], "conditionregexmatch": [0, 63], "conditionstartswith": 0, "conditionsubstr": [0, 3, 64, 65, 66, 67, 68], "config": [64, 66, 67, 68], "consid": 17, "construct": [9, 13, 15, 17, 20, 21], "contain": [11, 63], "contribut": 2, "convers": 25, "convert": [25, 47], "correspond": [17, 42, 43], "cost": 68, "count": [0, 46, 65, 68], "crd": [2, 6, 63], "creat": [3, 5, 11, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 60, 63], "csv": [11, 68], "current": 25, "custom": [5, 7, 9, 13, 15, 17, 66], "customlab": 64, "cycqueri": [0, 63, 64, 65, 66, 68], "d": 3, "dai": 21, "dask": 11, "data": [0, 3, 9, 11, 13, 15, 54, 67, 68], "databas": [2, 5, 7, 9, 10, 11, 13, 15, 17, 62, 63, 64, 65, 66, 67, 68], "dataclass": 11, "datafram": [3, 11], "dataset": [0, 5, 7, 9, 11, 13, 15, 17, 63], "datasetqueri": [0, 3, 7, 9, 13, 15, 17], "date": [25, 26, 27], "datetim": [5, 7, 9, 13, 15, 17, 21, 26, 27], "db": [0, 5, 65, 67], "dbm": [3, 5, 7, 9, 13, 15, 17, 64, 66, 67, 68], "dbname": 3, "dbsourc": 66, "dbtabl": [11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61], "dd": [26, 27], "death": 68, "default": [5, 11, 37], "defin": 11, "delirium_v4_0_1": 65, "delta": 21, "delta_kwarg": 20, "depend": 3, "derived_vari": 65, "descend": 52, "develop": 2, "device_exposur": 68, "df": 3, "di": 68, "diagnos": [0, 9, 13, 63], "diagnoses_icd": [0, 15, 67], "diagnoses_op": 67, "diagnosi": [9, 13, 15, 64], "diagnosisstr": 63, "dict": [46, 55], "dictionari": 46, "differ": [38, 47], "disabl": 24, "discharg": 63, "discharge_date_tim": 63, "discharge_to_concept_id": 68, "discharge_to_concept_nam": 68, "dischtim": 67, "distinct": [0, 3, 65], "doc": 3, "docstr": 1, "dod": 15, "domain": 68, "don": 1, "dose_era": 68, "downstream": [5, 7, 9, 13, 15, 17], "drop": [0, 58], "dropempti": [0, 65], "dropnul": [0, 3], "drug_era": 68, "drug_exposur": 68, "drug_strength": 68, "drugnam": 64, "dst_col": 17, "dt": 68, "dtype": 68, "dtype_backend": 11, "e": [3, 5, 44, 47, 50], "e501": 24, "each": [17, 24, 52, 63, 64, 66, 67, 68], "ehr": [3, 5, 62, 63, 68], "eicu": [0, 2, 63], "eicu_crd": 64, "eicuqueri": [0, 63], "electron": 3, "empti": [5, 42], "encount": [9, 63], "encounters_lab": 65, "encounters_per_sit": 65, "encounters_queri": 65, "end": [28, 58, 63], "env": 3, "environ": [1, 3], "episod": 68, "episode_ev": 68, "equal": [29, 30, 34], "er": 65, "erdiagnosi": 65, "erintervent": 65, "error": 1, "etl": 68, "event": [15, 63], "exampl": [19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 63], "execut": [58, 64, 65, 66, 67, 68], "exist": [19, 20, 21, 22, 55, 60], "expens": 47, "expire_flag": 66, "express": 36, "extend": [0, 58], "extract": [44, 59, 64, 65, 66, 67, 68], "extract_str": 44, "extracttimestampcompon": 0, "f": [64, 65, 66, 67, 68], "fact_relationship": 68, "fals": [11, 19, 20, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 52, 61, 65], "femal": 63, "fetch": [9, 11], "fhir_etl": 67, "fhir_trm": 67, "file": [1, 5, 11], "file_format": 11, "fill": [1, 45], "fill_valu": 45, "fillnul": 0, "filter": [3, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 63], "final": 58, "final_visit_id": 68, "finish": [64, 65, 66, 67, 68], "first": [61, 64, 66, 67, 68], "fix": 1, "flag": 47, "float": [22, 25], "follow": [57, 68], "forget": 1, "format": [1, 11, 26, 27, 47, 68], "framework": 11, "from": [3, 9, 11, 15, 17, 44, 47, 55, 60, 63, 64, 66, 68], "func": 24, "function": [15, 19, 20, 21, 22, 24, 46, 53, 60, 63, 64, 65, 66, 67, 68], "further": 1, "g": [3, 5, 44, 47, 50], "gastroenter": 63, "gemini": [0, 2, 63], "geminiqueri": [0, 63], "genc_id": 65, "gender": [64, 66, 67], "gender_concept_nam": 68, "gener": [11, 68], "get": [2, 5, 7, 9, 11, 13, 15, 17, 40, 59, 63], "get_tabl": [0, 5, 7, 9, 13, 15, 17], "given": [45, 58], "glucos": 63, "googl": 1, "greater": [30, 34], "group": 46, "groupbi": 3, "groupby_col": 46, "groupbyaggreg": [0, 65], "guid": 1, "guidelin": [2, 3], "ha": 59, "hadm_id": [66, 67], "have": [5, 7, 9, 13, 15, 17, 31, 38, 47, 63], "hba1c": [23, 35, 51], "health": 3, "hemoglobin": 63, "henc": 3, "hint": 1, "hook": 2, "hospit": [15, 63], "hospital_num": 65, "hospitaldischargeyear": 64, "hospitalid": 64, "host": [3, 5, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "hous": 68, "how": [63, 64, 66, 67, 68], "hpc": 65, "html": 3, "i": [1, 3, 5, 11, 15, 17, 19, 20, 21, 22, 24, 38, 42, 43, 47, 54, 63, 64, 66, 67, 68], "icd": 63, "icd_vers": 67, "icu": 15, "id": 17, "iii": [2, 12, 13, 63, 68], "imag": [0, 9], "implement": 53, "import": [3, 63], "includ": [3, 30, 34], "index": [11, 58, 59, 63], "index_col": [11, 67], "infecti": 63, "infer": 15, "info": [3, 9, 64, 65, 66, 67, 68], "inform": 44, "information_schema": [67, 68], "infusiondrug": 64, "initi": [11, 58], "input": 24, "insert": [0, 58], "instal": 2, "instanti": [5, 63], "instead": [23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 51], "instruct": [64, 66, 67, 68], "int": [5, 11, 22, 25, 32, 33, 47, 49, 58, 59], "int64": 68, "intakeoutput": 64, "integ": 50, "integr": 3, "intend": 5, "interest": 1, "interfac": [0, 9, 13, 15, 17], "interv": 20, "ip_admin": [0, 9], "ipdiagnosi": 65, "ipintervent": 65, "ipscu": 65, "isout": [11, 47, 68], "issu": 1, "iv": [2, 14, 63], "jane": [23, 51], "john": [23, 51], "join": [0, 3, 11, 15, 64, 65, 66, 67, 68], "join_tabl": [11, 47, 64, 66, 67, 68], "join_table_col": [11, 47], "just": 38, "keep": [0, 47, 63], "kei": [46, 55, 58], "keyword": [28, 29, 30, 31, 34, 37, 38, 61, 63], "kwarg": [53, 54], "lab": [15, 63, 65], "lab_nam": [23, 35, 46, 51], "lab_name_agg": 46, "lab_name_bool": 35, "lab_op": 65, "label": [19, 20, 21, 22, 44, 46, 50, 60, 66, 67], "labev": [0, 13, 15, 66], "labnam": 64, "lambda": 24, "larg": 54, "last": 1, "later": 63, "least": 1, "left": 47, "len": [64, 65, 66, 67, 68], "less": [34, 63], "like": [3, 17, 35], "limit": [0, 11, 54, 63, 66, 67, 68], "line": 24, "link": 1, "list": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 31, 32, 33, 38, 40, 41, 42, 43, 45, 46, 47, 48, 51, 52, 56, 57, 58, 60, 64, 65, 66, 67, 68], "list_column": [0, 5, 7, 9, 13, 15, 17], "list_custom_t": [0, 5, 7, 9, 13, 15, 17, 66], "list_schema": [0, 5, 7, 9, 13, 15, 17, 67, 68], "list_tabl": [0, 3, 5, 7, 9, 13, 15, 17, 64, 65, 68], "liter": [0, 11], "load": 68, "local": 3, "localhost": [3, 17, 64, 66, 67, 68], "locality_vari": 65, "locat": 68, "long": [24, 63], "long_titl": [66, 67], "lookup_cci": 65, "lookup_ccsr": 65, "lookup_diagnosi": 65, "lookup_er_administr": 65, "lookup_hospital_num": 65, "lookup_icd10_ca_descript": 65, "lookup_icd10_ca_to_ccsr": 65, "lookup_imag": 65, "lookup_ip_administr": 65, "lookup_ip_scu": 65, "lookup_lab_concept": 65, "lookup_pharmacy_concept": 65, "lookup_pharmacy_rout": 65, "lookup_phy_characterist": 65, "lookup_room_transf": 65, "lookup_statcan": 65, "lookup_transf": 65, "lookup_transfusion_concept": 65, "lookup_vitals_concept": 65, "lymphadenopathi": 63, "m": [3, 66], "mai": 63, "make": [3, 38], "male": 63, "manag": 5, "mani": [3, 63], "map": [5, 7, 9, 13, 15, 17, 55], "map_concept_ids_to_nam": [0, 17, 68], "march": 63, "match": [3, 36, 68], "measur": [0, 17, 63], "measurement_concept_nam": 68, "medic": 63, "metadata": 68, "method": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 66], "microlab": 64, "million": 11, "mimic": [2, 12, 13, 14, 15, 63, 68], "mimic_fhir": 67, "mimiciii": [0, 66, 68], "mimiciiiqueri": [0, 63, 68], "mimiciv": [0, 67], "mimiciv_": 67, "mimiciv_deriv": 67, "mimiciv_hosp": 67, "mimiciv_icu": 67, "mimiciv_not": 67, "mimicivqueri": [0, 63], "mm": [26, 27], "mode": 11, "model": 68, "modul": [6, 8, 12, 14, 15], "month": [32, 44], "more": 3, "mortal": 63, "most": 63, "multipl": [9, 23, 24, 46, 51], "must": [25, 31, 32, 33, 38, 46], "mypi": 1, "mysql": 5, "name": [5, 7, 9, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 51, 55, 56, 57, 59, 68], "nbsphinx_allow_error": 3, "need": [1, 59], "neg": [19, 20], "negat": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "neither": 47, "new": [19, 20, 21, 22, 24, 45, 46, 50, 56, 59, 60], "new_col": 24, "new_col_label": [19, 20, 21, 22, 59, 60], "new_col_nam": [45, 59], "next": 67, "none": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 52, 59, 60], "noqa": 24, "nor": 47, "not_": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "note": [5, 15, 64, 68], "note_nlp": 68, "notebook": [64, 65, 66, 67, 68], "null": [43, 45], "number": [5, 39, 49, 57, 63], "numer": 22, "numpi": 1, "nurseassess": 64, "nursecar": 64, "nursechart": 64, "object": [5, 9, 10, 11, 13, 15, 17, 20, 21, 24, 26, 27, 46, 53, 58, 63], "observ": [0, 17, 68], "observation_period": 68, "occur": 63, "omop": [0, 2, 63], "omopqueri": [0, 63], "on_to_typ": [11, 47], "onc": 1, "one": [38, 63], "onli": [38, 47, 48, 63], "op": [0, 3, 11, 15, 63, 64, 65, 66, 68], "op_": 58, "oper": [3, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "oppos": 47, "option": [5, 7, 9, 11, 13, 15, 17, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 61], "order": [3, 11, 52, 54, 56, 57], "orderbi": [0, 65], "ordereddict": 58, "origin": 11, "orm": [5, 11, 63, 64, 65, 66, 67, 68], "other": [11, 19, 57, 58], "otherwis": [19, 20, 21, 22, 60], "our": 1, "out": 1, "outcom": 63, "outer": [11, 47], "output": 68, "over": 46, "pai": 19, "pair": 46, "panda": [3, 11, 68], "paramet": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 64, 66, 67, 68], "parquet": 11, "partit": [11, 63], "pass": [64, 66, 67, 68], "password": [3, 5, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "pasthistori": 64, "path": [3, 5, 11], "patient": [0, 9, 15, 63], "patient_admiss": [66, 67], "patient_admissions_df": 67, "patient_admissions_diagnos": [66, 67], "patient_admissions_lab": 67, "patient_admissions_radiology_not": 67, "patient_admissions_vit": 67, "patient_chart_ev": 66, "patient_diagnos": 64, "patient_id_hash": 63, "patient_lab": [64, 66], "patient_med": 64, "patientunitstayid": 64, "pattern": 35, "payer_plan_period": 68, "pd": 68, "per": 63, "perform": [3, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 68], "person": [0, 17, 68], "person_id": [39, 40, 46, 68], "person_visit": 68, "person_visits_condit": 68, "person_visits_conditions_measur": 68, "pharmaci": 65, "physicalexam": 64, "pip": 2, "place": 63, "pleas": 1, "poetri": 2, "pop": [0, 58], "port": [3, 5, 7, 9, 13, 15, 17, 64, 66, 67, 68], "possibli": [5, 7, 9, 13, 15, 17], "postgr": [64, 66, 67, 68], "postgresql": [2, 5, 17, 63, 64, 66, 67, 68], "potassium": 63, "pr": 1, "pre": 2, "prevent": 46, "print": [64, 65, 66, 67, 68], "procedur": 15, "procedure_occurr": 68, "procedures_icd": [0, 15], "process": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61], "product": 47, "profil": [64, 65, 66, 67, 68], "properti": 11, "provid": [5, 7, 9, 13, 15, 17, 24, 38, 45, 46, 52, 62, 68], "public": [65, 67, 68], "pwd": [5, 64, 66, 67, 68], "pyarrow": [11, 68], "pylint": 24, "python": [1, 3, 63], "python3": 3, "qo": [3, 64, 65, 66, 67, 68], "queri": [2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 49, 51, 53, 58, 62, 63, 64, 65, 66, 67, 68], "querier": [3, 4, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "queryinterfac": [0, 9, 13, 15, 17], "queryop": [0, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61], "quick": [64, 66, 67, 68], "quit": 54, "r": 67, "radiologi": [63, 65], "radiology_not": 67, "radiology_notes_op": 67, "random": 54, "randomizeord": 0, "rather": [19, 20], "raw": 63, "readi": [64, 65, 66, 67, 68], "receiv": 15, "recent": 63, "recogn": [5, 7, 9, 13, 15, 17], "recommend": 1, "record": [3, 63], "refer": 2, "regex": 36, "regular": 36, "relat": 3, "relationship": 68, "releas": 68, "remov": [42, 43], "renam": 0, "rename_map": 55, "reorder": [0, 57], "reorderaft": 0, "repo": 68, "report": [9, 63], "repres": 47, "respiratorycar": 64, "respiratorychart": 64, "result": [11, 58, 64, 66, 67, 68], "return": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 68], "return_cond": [23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 51], "room": 9, "room_transf": [0, 9], "roomtransf": 65, "routin": 63, "row": [11, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 49, 52, 54, 63, 65, 66, 67, 68], "ruff": 1, "run": [0, 1, 3, 5, 11, 63, 64, 65, 66, 68], "run_queri": [64, 65, 66, 67, 68], "sai": 47, "same": [46, 47], "save": [0, 11], "schema": [3, 5, 7, 9, 13, 15, 17, 67, 68], "schema_nam": [5, 7, 9, 13, 15, 17, 68], "schizophrenia": 63, "search": 63, "see": 3, "seen": 54, "select": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 67], "self": 5, "separ": 46, "sepsi": 63, "sequenc": [46, 58], "sequenti": [0, 3, 11, 64, 65, 66, 67, 68], "server": 11, "set": [3, 11, 63], "setup": [1, 64, 65, 66, 67, 68], "should": 11, "show": [1, 64, 65, 66, 67, 68], "showcas": 68, "sign": 63, "simpl": 3, "singl": 24, "size": 11, "slice": 58, "slow": 54, "so": 54, "sodium": 63, "sodium_test": 65, "some": [3, 19, 20, 21, 22, 26, 27, 28, 29, 30, 34, 37, 41, 42, 43, 52, 55, 60], "somecol_concept_id": 17, "somecol_concept_nam": 17, "somet": 3, "sort": [52, 63], "sort_index": 68, "sourc": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "source_to_concept_map": 68, "source_to_source_vocab_map": 68, "source_to_standard_vocab_map": 68, "specif": 3, "specifi": [17, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 46, 47, 48, 57, 60], "specimen": 68, "sphinx": 3, "sphinxopt": 3, "sql": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 63], "sqlalchemi": [3, 5, 7, 9, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 63], "sqlite": 5, "src_col": 17, "src_tabl": 17, "standard": [5, 7, 9, 13, 15, 17], "start": [2, 37, 59], "start_index": 59, "static": 1, "stop": 59, "stop_index": 59, "str": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 52, 55, 56, 57, 58, 59, 60, 67], "string": [28, 37, 46, 47, 50, 59, 60, 63], "string_agg": 46, "string_aggfunc": 46, "style": [1, 47], "subclass": 5, "subject_id": [63, 66], "submit": 1, "subqueri": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "subset": 63, "substr": [0, 3, 38, 63], "subtract": [19, 20], "successfulli": [64, 65, 66, 67, 68], "suggest": 47, "suppli": 15, "support": [6, 12, 14, 25], "sure": 3, "synthea": 68, "synthea_integration_test": 68, "system": 5, "t": 1, "tabl": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 66, 68], "table1": [47, 61], "table2": [47, 61], "table_col": [11, 47], "table_nam": [5, 7, 9, 13, 15, 17], "take": [24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 63], "teach": 63, "teachingstatu": 64, "templat": 1, "test": [3, 63], "test_type_map": 65, "text": 67, "than": [19, 20, 30, 34, 63], "thank": 1, "them": 11, "thi": [5, 22, 38, 46, 47, 64, 65, 66, 67, 68], "thu": 11, "time": 44, "timedelta": 21, "timestamp": [5, 7, 9, 13, 15, 17, 25, 26, 27, 32, 33, 44, 65], "timestamp_col": [26, 27, 32, 33, 44], "titl": 63, "to_datetim": 68, "togeth": 63, "too": 24, "tool": [1, 3, 63, 64, 65, 66, 67, 68], "total": 63, "transfer": 9, "transfus": 65, "treatment": 64, "trim": 0, "true": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 35, 38, 52, 55, 61, 64, 65, 67, 68], "tupl": [11, 47], "tutori": 2, "two": [47, 58, 61], "type": [1, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "type_": 25, "union": [0, 5, 11, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60], "union_al": [0, 11, 61], "union_t": 61, "unit": [3, 9], "up": 3, "updat": [64, 66, 67, 68], "upstream": 11, "urin": 68, "us": [1, 2, 5, 7, 9, 11, 13, 15, 17, 20, 23, 40, 46, 47, 51, 54, 61, 63, 64, 65, 66, 68], "usenam": 3, "user": [3, 5, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "usernam": [5, 64, 65, 66, 67, 68], "util": [64, 65, 66, 67, 68], "v1": [66, 68], "v2": [67, 68], "valu": [22, 29, 30, 31, 34, 42, 43, 45, 46, 47, 50], "value_count": 68, "valuenum": 63, "virtual": 1, "visit": 63, "visit_count": 46, "visit_detail": [0, 17, 68], "visit_id": 40, "visit_occurr": [0, 17, 68], "visit_occurrence_id": 68, "visit_start_d": 68, "visits_concept_map": 68, "visits_concept_mapped_di": 68, "visits_measur": 68, "vital": [63, 65], "vitalaperiod": 64, "vitalperiod": 64, "vocabulari": 68, "we": [1, 68], "weight": 68, "welcom": 3, "were": 63, "when": [5, 38, 47, 54], "where": [11, 59], "wherea": 19, "whether": [5, 7, 9, 11, 13, 15, 17, 38, 52, 55, 61], "which": [1, 5, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 68], "whitespac": 60, "who": 63, "work": 19, "wrap": [9, 10, 11, 13, 15, 17], "wrapper": [3, 63], "write": 3, "x": 24, "y": 24, "year": [15, 32, 33, 44, 63, 68], "you": [1, 63], "your": 1, "yyyi": [26, 27]}, "titles": ["API Reference", "Contributing to cycquery", "Welcome to cycquery\u2019s documentation!", "cycquery", "cycquery.base", "cycquery.base.DatasetQuerier", "cycquery.eicu", "cycquery.eicu.EICUQuerier", "cycquery.gemini", "cycquery.gemini.GEMINIQuerier", "cycquery.interface", "cycquery.interface.QueryInterface", "cycquery.mimiciii", "cycquery.mimiciii.MIMICIIIQuerier", "cycquery.mimiciv", "cycquery.mimiciv.MIMICIVQuerier", "cycquery.omop", "cycquery.omop.OMOPQuerier", "cycquery.ops", "cycquery.ops.AddColumn", "cycquery.ops.AddDeltaColumn", "cycquery.ops.AddDeltaConstant", "cycquery.ops.AddNumeric", "cycquery.ops.And", "cycquery.ops.Apply", "cycquery.ops.Cast", "cycquery.ops.ConditionAfterDate", "cycquery.ops.ConditionBeforeDate", "cycquery.ops.ConditionEndsWith", "cycquery.ops.ConditionEquals", "cycquery.ops.ConditionGreaterThan", "cycquery.ops.ConditionIn", "cycquery.ops.ConditionInMonths", "cycquery.ops.ConditionInYears", "cycquery.ops.ConditionLessThan", "cycquery.ops.ConditionLike", "cycquery.ops.ConditionRegexMatch", "cycquery.ops.ConditionStartsWith", "cycquery.ops.ConditionSubstring", "cycquery.ops.Count", "cycquery.ops.Distinct", "cycquery.ops.Drop", "cycquery.ops.DropEmpty", "cycquery.ops.DropNulls", "cycquery.ops.ExtractTimestampComponent", "cycquery.ops.FillNull", "cycquery.ops.GroupByAggregate", "cycquery.ops.Join", "cycquery.ops.Keep", "cycquery.ops.Limit", "cycquery.ops.Literal", "cycquery.ops.Or", "cycquery.ops.OrderBy", "cycquery.ops.QueryOp", "cycquery.ops.RandomizeOrder", "cycquery.ops.Rename", "cycquery.ops.Reorder", "cycquery.ops.ReorderAfter", "cycquery.ops.Sequential", "cycquery.ops.Substring", "cycquery.ops.Trim", "cycquery.ops.Union", "cycquery", "Tutorials", "eICU-CRD tutorial", "GEMINI tutorial", "MIMIC-III tutorial", "MIMIC-IV tutorial", "OMOP tutorial"], "titleterms": {"": 2, "1": [64, 65, 66, 67, 68], "10": 67, "100": 64, "101": 65, "1a": 65, "1b": 65, "1c": 65, "2": [64, 66, 67, 68], "20": 66, "2009": 67, "2010": 68, "2014": 64, "2015": [64, 65, 67], "2016": 65, "2020": 68, "2021": 67, "2a": 65, "3": [64, 66, 67], "31": 65, "4": [64, 66, 67], "5": 67, "6": 67, "7": 67, "8": 67, "9": [66, 67], "And": 23, "Or": 51, "aado2": 66, "abov": 65, "addcolumn": 19, "adddeltacolumn": 20, "adddeltaconst": 21, "addnumer": 22, "admiss": [65, 67], "advanc": 67, "after": 68, "all": [64, 66, 67, 68], "api": [0, 62], "appli": 24, "approx": 67, "apr": 65, "april": 65, "base": [4, 5], "batch": 67, "between": 65, "carevu": 66, "cast": 25, "chart": 66, "chronic": 67, "code": 1, "commit": 1, "conditionafterd": 26, "conditionbefored": 27, "conditionendswith": 28, "conditionequ": 29, "conditiongreaterthan": 30, "conditionin": 31, "conditioninmonth": 32, "conditioninyear": 33, "conditionlessthan": 34, "conditionlik": 35, "conditionregexmatch": [36, 67], "conditionstartswith": 37, "conditionsubstr": 38, "contain": 67, "content": 2, "contribut": [1, 3], "count": 39, "crd": 64, "creat": 65, "cycqueri": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 67], "databas": 3, "dataset": [62, 65], "datasetqueri": 5, "develop": 3, "diagnos": [64, 66, 67, 68], "diagnosisstr": 64, "discharg": [64, 65], "discharge_date_tim": 65, "distinct": 40, "document": [2, 3], "drop": 41, "dropempti": 42, "dropnul": 43, "each": 65, "eicu": [6, 7, 64], "eicuqueri": [7, 64], "encount": [64, 65, 66, 67], "end": 68, "event": 66, "exampl": [64, 65, 66, 67, 68], "extracttimestampcompon": 44, "femal": [64, 66, 67, 68], "fillnul": 45, "filter": 67, "from": [65, 67], "gastroenter": 66, "gemini": [8, 9, 65], "geminiqueri": [9, 65], "get": [3, 64, 65, 66, 67, 68], "glucos": 64, "groupbyaggreg": 46, "guidelin": 1, "have": 66, "hemoglobin": 67, "hook": 1, "hospit": [64, 65], "how": 65, "icd": [66, 67], "iii": 66, "import": [64, 65, 66, 67, 68], "index": 67, "infecti": 67, "instal": 3, "instanti": [64, 65, 66, 67, 68], "interfac": [10, 11], "iv": 67, "join": 47, "keep": [48, 65], "keyword": 67, "lab": [64, 66, 67], "later": 67, "less": 66, "limit": [49, 64], "liter": 50, "long": [66, 67], "lymphadenopathi": 67, "mai": 65, "male": 66, "mani": 65, "march": 65, "measur": 68, "medic": 64, "mimic": [66, 67], "mimiciii": [12, 13], "mimiciiiqueri": [13, 66], "mimiciv": [14, 15], "mimicivqueri": [15, 67], "mortal": [66, 68], "most": 65, "number": 65, "occur": 67, "omop": [16, 17, 68], "omopqueri": [17, 68], "one": 65, "onli": 65, "op": [18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 67], "orderbi": 52, "outcom": [66, 68], "partit": 67, "patient": [64, 65, 66, 67, 68], "patient_id_hash": 65, "per": 65, "pip": 3, "place": 65, "poetri": 3, "postgresql": 3, "potassium": [64, 66], "pre": 1, "queri": 3, "queryinterfac": 11, "queryop": 53, "radiologi": 67, "randomizeord": 54, "raw": 67, "recent": 65, "record": 65, "refer": 0, "renam": 55, "reorder": 56, "reorderaft": 57, "report": 67, "return": 67, "routin": 67, "row": 64, "run": 67, "schizophrenia": [64, 67], "search": 64, "sepsi": 68, "sequenti": 58, "set": 65, "sign": 67, "sodium": 65, "sort": 65, "sql": 67, "start": 3, "string": 67, "subject_id": 67, "subset": 65, "substr": [59, 64], "tabl": 65, "take": 65, "teach": 64, "test": [64, 65, 66, 67], "than": 66, "titl": [66, 67], "togeth": 67, "total": 65, "trim": 60, "tutori": [63, 64, 65, 66, 67, 68], "union": 61, "us": [3, 67], "valuenum": 66, "visit": 68, "vital": 67, "welcom": 2, "were": 65, "who": 65, "year": [64, 67]}}) \ No newline at end of file +Search.setIndex({"alltitles": {"API Reference": [[0, "api-reference"]], "Coding guidelines": [[1, "coding-guidelines"]], "Contents:": [[2, null]], "Contributing": [[3, "contributing"]], "Contributing to cycquery": [[1, "contributing-to-cycquery"]], "Example 1. Get all female patients discharged in 2014 (limit to 100 rows).": [[64, "Example-1.-Get-all-female-patients-discharged-in-2014-(limit-to-100-rows)."]], "Example 1. Get all male patients with a mortality outcome.": [[66, "Example-1.-Get-all-male-patients-with-a-mortality-outcome."]], "Example 1. Get all patient admissions from 2021 or later (approx year of admission)": [[67, "Example-1.-Get-all-patient-admissions-from-2021-or-later-(approx-year-of-admission)"]], "Example 1. Get all patient visits in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-in-or-after-2010."]], "Example 1. Get all patient visits that ended in a mortality outcome in or after 2010.": [[68, "Example-1.-Get-all-patient-visits-that-ended-in-a-mortality-outcome-in-or-after-2010."]], "Example 1a. Create a table with only one hospitalization per patient, keeping the most recent encounter for each patient. Sort the dataset by patient_id_hashed and discharge_date_time, and then keep the recent record.": [[65, "Example-1a.-Create-a-table-with-only-one-hospitalization-per-patient,-keeping-the-most-recent-encounter-for-each-patient.-Sort-the-dataset-by-patient_id_hashed-and-discharge_date_time,-and-then-keep-the-recent-record."]], "Example 1b. From the above set of encounters, take a subset of patients who were discharged between April 1, 2015 and March 31, 2016.": [[65, "Example-1b.-From-the-above-set-of-encounters,-take-a-subset-of-patients-who-were-discharged-between-April-1,-2015-and-March-31,-2016."]], "Example 1c. From the above set of encounters, get the total number of admissions for each hospital.": [[65, "Example-1c.-From-the-above-set-of-encounters,-get-the-total-number-of-admissions-for-each-hospital."]], "Example 2. Get all female patient encounters with diagnoses (gastroenteritis in ICD-9 long title).": [[66, "Example-2.-Get-all-female-patient-encounters-with-diagnoses-(gastroenteritis-in-ICD-9-long-title)."]], "Example 2. Get all measurements for female patient visits with sepsis diagnoses, that ended in a mortality outcome.": [[68, "Example-2.-Get-all-measurements-for-female-patient-visits-with-sepsis-diagnoses,-that-ended-in-a-mortality-outcome."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in ICD-10 long title), in the year 2015.": [[67, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-ICD-10-long-title),-in-the-year-2015."]], "Example 2. Get all patient encounters with diagnoses (schizophrenia in diagnosisstring), discharged in the year 2015.": [[64, "Example-2.-Get-all-patient-encounters-with-diagnoses-(schizophrenia-in-diagnosisstring),-discharged-in-the-year-2015."]], "Example 2. Get measurements for all visits in or after 2020.": [[68, "Example-2.-Get-measurements-for-all-visits-in-or-after-2020."]], "Example 2a. How many sodium tests were placed between Apr 1, 2015 and May 31, 2015 at hospital 101?": [[65, "Example-2a.-How-many-sodium-tests-were-placed-between-Apr-1,-2015-and-May-31,-2015-at-hospital-101?"]], "Example 3. Advanced - uses ConditionRegexMatch from cycquery.ops. Get all patient encounters with diagnoses (ICD-9 long title contains schizophrenia and chronic ), in the year 2015.": [[67, "Example-3.-Advanced---uses-ConditionRegexMatch-from-cycquery.ops.-Get-all-patient-encounters-with-diagnoses-(ICD-9-long-title-contains-schizophrenia-and-chronic-),-in-the-year-2015."]], "Example 3. Get potassium lab tests for female patients.": [[66, "Example-3.-Get-potassium-lab-tests-for-female-patients."]], "Example 3. Get potassium lab tests for patients discharged in the year 2014, for all teaching hospitals.": [[64, "Example-3.-Get-potassium-lab-tests-for-patients-discharged-in-the-year-2014,-for-all-teaching-hospitals."]], "Example 4. Get AaDO2 carevue chart events for male patients that have a valuenum of less than 20.": [[66, "Example-4.-Get-AaDO2-carevue-chart-events-for-male-patients-that-have-a-valuenum-of-less-than-20."]], "Example 4. Get glucose medications (substring search) for female patients discharged in 2014.": [[64, "Example-4.-Get-glucose-medications-(substring-search)-for-female-patients-discharged-in-2014."]], "Example 4. Get routine vital signs for patients from year 2015.": [[67, "Example-4.-Get-routine-vital-signs-for-patients-from-year-2015."]], "Example 5. Get hemoglobin lab tests for patients from year 2009.": [[67, "Example-5.-Get-hemoglobin-lab-tests-for-patients-from-year-2009."]], "Example 6. Get radiology reports and filter on keywords lymphadenopathy and infectious occurring together from year 2009.": [[67, "Example-6.-Get-radiology-reports-and-filter-on-keywords-lymphadenopathy-and-infectious-occurring-together-from-year-2009."]], "Example 7. Get all female patient encounters from year 2015, and return batches partitioned and indexed on subject_id.": [[67, "Example-7.-Get-all-female-patient-encounters-from-year-2015,-and-return-batches-partitioned-and-indexed-on-subject_id."]], "Example 8. Running a raw SQL string.": [[67, "Example-8.-Running-a-raw-SQL-string."]], "GEMINI tutorial": [[65, "GEMINI-tutorial"]], "Imports and instantiate EICUQuerier": [[64, "Imports-and-instantiate-EICUQuerier"]], "Imports and instantiate GEMINIQuerier.": [[65, "Imports-and-instantiate-GEMINIQuerier."]], "Imports and instantiate MIMICIIIQuerier": [[66, "Imports-and-instantiate-MIMICIIIQuerier"]], "Imports and instantiate MIMICIVQuerier": [[67, "Imports-and-instantiate-MIMICIVQuerier"]], "Imports and instantiate OMOPQuerier.": [[68, "Imports-and-instantiate-OMOPQuerier."], [68, "id1"]], "Installing cycquery using pip": [[3, "installing-cycquery-using-pip"]], "MIMIC-III tutorial": [[66, "MIMIC-III-tutorial"]], "MIMIC-IV tutorial": [[67, "MIMIC-IV-tutorial"]], "OMOP tutorial": [[68, "OMOP-tutorial"]], "Pre-commit hooks": [[1, "pre-commit-hooks"]], "Query postgresql database": [[3, "query-postgresql-database"]], "Tutorials": [[63, "tutorials"]], "Using poetry": [[3, "using-poetry"]], "Welcome to cycquery\u2019s documentation!": [[2, "welcome-to-cycquery-s-documentation"]], "cycquery": [[3, "cycquery"], [62, "module-cycquery"]], "cycquery.base": [[4, "module-cycquery.base"]], "cycquery.base.DatasetQuerier": [[5, "cycquery-base-datasetquerier"]], "cycquery.eicu": [[6, "module-cycquery.eicu"]], "cycquery.eicu.EICUQuerier": [[7, "cycquery-eicu-eicuquerier"]], "cycquery.gemini": [[8, "module-cycquery.gemini"]], "cycquery.gemini.GEMINIQuerier": [[9, "cycquery-gemini-geminiquerier"]], "cycquery.interface": [[10, "module-cycquery.interface"]], "cycquery.interface.QueryInterface": [[11, "cycquery-interface-queryinterface"]], "cycquery.mimiciii": [[12, "module-cycquery.mimiciii"]], "cycquery.mimiciii.MIMICIIIQuerier": [[13, "cycquery-mimiciii-mimiciiiquerier"]], "cycquery.mimiciv": [[14, "module-cycquery.mimiciv"]], "cycquery.mimiciv.MIMICIVQuerier": [[15, "cycquery-mimiciv-mimicivquerier"]], "cycquery.omop": [[16, "module-cycquery.omop"]], "cycquery.omop.OMOPQuerier": [[17, "cycquery-omop-omopquerier"]], "cycquery.ops": [[18, "module-cycquery.ops"]], "cycquery.ops.AddColumn": [[19, "cycquery-ops-addcolumn"]], "cycquery.ops.AddDeltaColumn": [[20, "cycquery-ops-adddeltacolumn"]], "cycquery.ops.AddDeltaConstant": [[21, "cycquery-ops-adddeltaconstant"]], "cycquery.ops.AddNumeric": [[22, "cycquery-ops-addnumeric"]], "cycquery.ops.And": [[23, "cycquery-ops-and"]], "cycquery.ops.Apply": [[24, "cycquery-ops-apply"]], "cycquery.ops.Cast": [[25, "cycquery-ops-cast"]], "cycquery.ops.ConditionAfterDate": [[26, "cycquery-ops-conditionafterdate"]], "cycquery.ops.ConditionBeforeDate": [[27, "cycquery-ops-conditionbeforedate"]], "cycquery.ops.ConditionEndsWith": [[28, "cycquery-ops-conditionendswith"]], "cycquery.ops.ConditionEquals": [[29, "cycquery-ops-conditionequals"]], "cycquery.ops.ConditionGreaterThan": [[30, "cycquery-ops-conditiongreaterthan"]], "cycquery.ops.ConditionIn": [[31, "cycquery-ops-conditionin"]], "cycquery.ops.ConditionInMonths": [[32, "cycquery-ops-conditioninmonths"]], "cycquery.ops.ConditionInYears": [[33, "cycquery-ops-conditioninyears"]], "cycquery.ops.ConditionLessThan": [[34, "cycquery-ops-conditionlessthan"]], "cycquery.ops.ConditionLike": [[35, "cycquery-ops-conditionlike"]], "cycquery.ops.ConditionRegexMatch": [[36, "cycquery-ops-conditionregexmatch"]], "cycquery.ops.ConditionStartsWith": [[37, "cycquery-ops-conditionstartswith"]], "cycquery.ops.ConditionSubstring": [[38, "cycquery-ops-conditionsubstring"]], "cycquery.ops.Count": [[39, "cycquery-ops-count"]], "cycquery.ops.Distinct": [[40, "cycquery-ops-distinct"]], "cycquery.ops.Drop": [[41, "cycquery-ops-drop"]], "cycquery.ops.DropEmpty": [[42, "cycquery-ops-dropempty"]], "cycquery.ops.DropNulls": [[43, "cycquery-ops-dropnulls"]], "cycquery.ops.ExtractTimestampComponent": [[44, "cycquery-ops-extracttimestampcomponent"]], "cycquery.ops.FillNull": [[45, "cycquery-ops-fillnull"]], "cycquery.ops.GroupByAggregate": [[46, "cycquery-ops-groupbyaggregate"]], "cycquery.ops.Join": [[47, "cycquery-ops-join"]], "cycquery.ops.Keep": [[48, "cycquery-ops-keep"]], "cycquery.ops.Limit": [[49, "cycquery-ops-limit"]], "cycquery.ops.Literal": [[50, "cycquery-ops-literal"]], "cycquery.ops.Or": [[51, "cycquery-ops-or"]], "cycquery.ops.OrderBy": [[52, "cycquery-ops-orderby"]], "cycquery.ops.QueryOp": [[53, "cycquery-ops-queryop"]], "cycquery.ops.RandomizeOrder": [[54, "cycquery-ops-randomizeorder"]], "cycquery.ops.Rename": [[55, "cycquery-ops-rename"]], "cycquery.ops.Reorder": [[56, "cycquery-ops-reorder"]], "cycquery.ops.ReorderAfter": [[57, "cycquery-ops-reorderafter"]], "cycquery.ops.Sequential": [[58, "cycquery-ops-sequential"]], "cycquery.ops.Substring": [[59, "cycquery-ops-substring"]], "cycquery.ops.Trim": [[60, "cycquery-ops-trim"]], "cycquery.ops.Union": [[61, "cycquery-ops-union"]], "dataset APIs": [[62, "dataset-apis"]], "eICU-CRD tutorial": [[64, "eICU-CRD-tutorial"]], "\ud83d\udc23 Getting Started": [[3, "getting-started"]], "\ud83d\udcda Documentation": [[3, "documentation"]], "\ud83e\uddd1\ud83c\udfff\u200d\ud83d\udcbb Developing": [[3, "developing"]]}, "docnames": ["api", "contributing", "index", "intro", "reference/api/_autosummary/cycquery.base", "reference/api/_autosummary/cycquery.base.DatasetQuerier", "reference/api/_autosummary/cycquery.eicu", "reference/api/_autosummary/cycquery.eicu.EICUQuerier", "reference/api/_autosummary/cycquery.gemini", "reference/api/_autosummary/cycquery.gemini.GEMINIQuerier", "reference/api/_autosummary/cycquery.interface", "reference/api/_autosummary/cycquery.interface.QueryInterface", "reference/api/_autosummary/cycquery.mimiciii", "reference/api/_autosummary/cycquery.mimiciii.MIMICIIIQuerier", "reference/api/_autosummary/cycquery.mimiciv", "reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier", "reference/api/_autosummary/cycquery.omop", "reference/api/_autosummary/cycquery.omop.OMOPQuerier", "reference/api/_autosummary/cycquery.ops", "reference/api/_autosummary/cycquery.ops.AddColumn", "reference/api/_autosummary/cycquery.ops.AddDeltaColumn", "reference/api/_autosummary/cycquery.ops.AddDeltaConstant", "reference/api/_autosummary/cycquery.ops.AddNumeric", "reference/api/_autosummary/cycquery.ops.And", "reference/api/_autosummary/cycquery.ops.Apply", "reference/api/_autosummary/cycquery.ops.Cast", "reference/api/_autosummary/cycquery.ops.ConditionAfterDate", "reference/api/_autosummary/cycquery.ops.ConditionBeforeDate", "reference/api/_autosummary/cycquery.ops.ConditionEndsWith", "reference/api/_autosummary/cycquery.ops.ConditionEquals", "reference/api/_autosummary/cycquery.ops.ConditionGreaterThan", "reference/api/_autosummary/cycquery.ops.ConditionIn", "reference/api/_autosummary/cycquery.ops.ConditionInMonths", "reference/api/_autosummary/cycquery.ops.ConditionInYears", "reference/api/_autosummary/cycquery.ops.ConditionLessThan", "reference/api/_autosummary/cycquery.ops.ConditionLike", "reference/api/_autosummary/cycquery.ops.ConditionRegexMatch", "reference/api/_autosummary/cycquery.ops.ConditionStartsWith", "reference/api/_autosummary/cycquery.ops.ConditionSubstring", "reference/api/_autosummary/cycquery.ops.Count", "reference/api/_autosummary/cycquery.ops.Distinct", "reference/api/_autosummary/cycquery.ops.Drop", "reference/api/_autosummary/cycquery.ops.DropEmpty", "reference/api/_autosummary/cycquery.ops.DropNulls", "reference/api/_autosummary/cycquery.ops.ExtractTimestampComponent", "reference/api/_autosummary/cycquery.ops.FillNull", "reference/api/_autosummary/cycquery.ops.GroupByAggregate", "reference/api/_autosummary/cycquery.ops.Join", "reference/api/_autosummary/cycquery.ops.Keep", "reference/api/_autosummary/cycquery.ops.Limit", "reference/api/_autosummary/cycquery.ops.Literal", "reference/api/_autosummary/cycquery.ops.Or", "reference/api/_autosummary/cycquery.ops.OrderBy", "reference/api/_autosummary/cycquery.ops.QueryOp", "reference/api/_autosummary/cycquery.ops.RandomizeOrder", "reference/api/_autosummary/cycquery.ops.Rename", "reference/api/_autosummary/cycquery.ops.Reorder", "reference/api/_autosummary/cycquery.ops.ReorderAfter", "reference/api/_autosummary/cycquery.ops.Sequential", "reference/api/_autosummary/cycquery.ops.Substring", "reference/api/_autosummary/cycquery.ops.Trim", "reference/api/_autosummary/cycquery.ops.Union", "reference/api/cycquery", "tutorials", "tutorials/eicu", "tutorials/gemini", "tutorials/mimiciii", "tutorials/mimiciv", "tutorials/omop"], "envversion": {"nbsphinx": 4, "sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1}, "filenames": ["api.rst", "contributing.rst", "index.rst", "intro.rst", "reference/api/_autosummary/cycquery.base.rst", "reference/api/_autosummary/cycquery.base.DatasetQuerier.rst", "reference/api/_autosummary/cycquery.eicu.rst", "reference/api/_autosummary/cycquery.eicu.EICUQuerier.rst", "reference/api/_autosummary/cycquery.gemini.rst", "reference/api/_autosummary/cycquery.gemini.GEMINIQuerier.rst", "reference/api/_autosummary/cycquery.interface.rst", "reference/api/_autosummary/cycquery.interface.QueryInterface.rst", "reference/api/_autosummary/cycquery.mimiciii.rst", "reference/api/_autosummary/cycquery.mimiciii.MIMICIIIQuerier.rst", "reference/api/_autosummary/cycquery.mimiciv.rst", "reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.rst", "reference/api/_autosummary/cycquery.omop.rst", "reference/api/_autosummary/cycquery.omop.OMOPQuerier.rst", "reference/api/_autosummary/cycquery.ops.rst", "reference/api/_autosummary/cycquery.ops.AddColumn.rst", "reference/api/_autosummary/cycquery.ops.AddDeltaColumn.rst", "reference/api/_autosummary/cycquery.ops.AddDeltaConstant.rst", "reference/api/_autosummary/cycquery.ops.AddNumeric.rst", "reference/api/_autosummary/cycquery.ops.And.rst", "reference/api/_autosummary/cycquery.ops.Apply.rst", "reference/api/_autosummary/cycquery.ops.Cast.rst", "reference/api/_autosummary/cycquery.ops.ConditionAfterDate.rst", "reference/api/_autosummary/cycquery.ops.ConditionBeforeDate.rst", "reference/api/_autosummary/cycquery.ops.ConditionEndsWith.rst", "reference/api/_autosummary/cycquery.ops.ConditionEquals.rst", "reference/api/_autosummary/cycquery.ops.ConditionGreaterThan.rst", "reference/api/_autosummary/cycquery.ops.ConditionIn.rst", "reference/api/_autosummary/cycquery.ops.ConditionInMonths.rst", "reference/api/_autosummary/cycquery.ops.ConditionInYears.rst", "reference/api/_autosummary/cycquery.ops.ConditionLessThan.rst", "reference/api/_autosummary/cycquery.ops.ConditionLike.rst", "reference/api/_autosummary/cycquery.ops.ConditionRegexMatch.rst", "reference/api/_autosummary/cycquery.ops.ConditionStartsWith.rst", "reference/api/_autosummary/cycquery.ops.ConditionSubstring.rst", "reference/api/_autosummary/cycquery.ops.Count.rst", "reference/api/_autosummary/cycquery.ops.Distinct.rst", "reference/api/_autosummary/cycquery.ops.Drop.rst", "reference/api/_autosummary/cycquery.ops.DropEmpty.rst", "reference/api/_autosummary/cycquery.ops.DropNulls.rst", "reference/api/_autosummary/cycquery.ops.ExtractTimestampComponent.rst", "reference/api/_autosummary/cycquery.ops.FillNull.rst", "reference/api/_autosummary/cycquery.ops.GroupByAggregate.rst", "reference/api/_autosummary/cycquery.ops.Join.rst", "reference/api/_autosummary/cycquery.ops.Keep.rst", "reference/api/_autosummary/cycquery.ops.Limit.rst", "reference/api/_autosummary/cycquery.ops.Literal.rst", "reference/api/_autosummary/cycquery.ops.Or.rst", "reference/api/_autosummary/cycquery.ops.OrderBy.rst", "reference/api/_autosummary/cycquery.ops.QueryOp.rst", "reference/api/_autosummary/cycquery.ops.RandomizeOrder.rst", "reference/api/_autosummary/cycquery.ops.Rename.rst", "reference/api/_autosummary/cycquery.ops.Reorder.rst", "reference/api/_autosummary/cycquery.ops.ReorderAfter.rst", "reference/api/_autosummary/cycquery.ops.Sequential.rst", "reference/api/_autosummary/cycquery.ops.Substring.rst", "reference/api/_autosummary/cycquery.ops.Trim.rst", "reference/api/_autosummary/cycquery.ops.Union.rst", "reference/api/cycquery.rst", "tutorials.rst", "tutorials/eicu.ipynb", "tutorials/gemini.ipynb", "tutorials/mimiciii.ipynb", "tutorials/mimiciv.ipynb", "tutorials/omop.ipynb"], "indexentries": {"__add__() (sequential method)": [[58, "cycquery.ops.Sequential.__add__", false]], "__call__() (addcolumn method)": [[19, "cycquery.ops.AddColumn.__call__", false]], "__call__() (adddeltacolumn method)": [[20, "cycquery.ops.AddDeltaColumn.__call__", false]], "__call__() (adddeltaconstant method)": [[21, "cycquery.ops.AddDeltaConstant.__call__", false]], "__call__() (addnumeric method)": [[22, "cycquery.ops.AddNumeric.__call__", false]], "__call__() (and method)": [[23, "cycquery.ops.And.__call__", false]], "__call__() (apply method)": [[24, "cycquery.ops.Apply.__call__", false]], "__call__() (cast method)": [[25, "cycquery.ops.Cast.__call__", false]], "__call__() (conditionafterdate method)": [[26, "cycquery.ops.ConditionAfterDate.__call__", false]], "__call__() (conditionbeforedate method)": [[27, "cycquery.ops.ConditionBeforeDate.__call__", false]], "__call__() (conditionendswith method)": [[28, "cycquery.ops.ConditionEndsWith.__call__", false]], "__call__() (conditionequals method)": [[29, "cycquery.ops.ConditionEquals.__call__", false]], "__call__() (conditiongreaterthan method)": [[30, "cycquery.ops.ConditionGreaterThan.__call__", false]], "__call__() (conditionin method)": [[31, "cycquery.ops.ConditionIn.__call__", false]], "__call__() (conditioninmonths method)": [[32, "cycquery.ops.ConditionInMonths.__call__", false]], "__call__() (conditioninyears method)": [[33, "cycquery.ops.ConditionInYears.__call__", false]], "__call__() (conditionlessthan method)": [[34, "cycquery.ops.ConditionLessThan.__call__", false]], "__call__() (conditionlike method)": [[35, "cycquery.ops.ConditionLike.__call__", false]], "__call__() (conditionregexmatch method)": [[36, "cycquery.ops.ConditionRegexMatch.__call__", false]], "__call__() (conditionstartswith method)": [[37, "cycquery.ops.ConditionStartsWith.__call__", false]], "__call__() (conditionsubstring method)": [[38, "cycquery.ops.ConditionSubstring.__call__", false]], "__call__() (count method)": [[39, "cycquery.ops.Count.__call__", false]], "__call__() (distinct method)": [[40, "cycquery.ops.Distinct.__call__", false]], "__call__() (drop method)": [[41, "cycquery.ops.Drop.__call__", false]], "__call__() (dropempty method)": [[42, "cycquery.ops.DropEmpty.__call__", false]], "__call__() (dropnulls method)": [[43, "cycquery.ops.DropNulls.__call__", false]], "__call__() (extracttimestampcomponent method)": [[44, "cycquery.ops.ExtractTimestampComponent.__call__", false]], "__call__() (fillnull method)": [[45, "cycquery.ops.FillNull.__call__", false]], "__call__() (groupbyaggregate method)": [[46, "cycquery.ops.GroupByAggregate.__call__", false]], "__call__() (join method)": [[47, "cycquery.ops.Join.__call__", false]], "__call__() (keep method)": [[48, "cycquery.ops.Keep.__call__", false]], "__call__() (limit method)": [[49, "cycquery.ops.Limit.__call__", false]], "__call__() (literal method)": [[50, "cycquery.ops.Literal.__call__", false]], "__call__() (or method)": [[51, "cycquery.ops.Or.__call__", false]], "__call__() (orderby method)": [[52, "cycquery.ops.OrderBy.__call__", false]], "__call__() (queryop method)": [[53, "cycquery.ops.QueryOp.__call__", false]], "__call__() (randomizeorder method)": [[54, "cycquery.ops.RandomizeOrder.__call__", false]], "__call__() (rename method)": [[55, "cycquery.ops.Rename.__call__", false]], "__call__() (reorder method)": [[56, "cycquery.ops.Reorder.__call__", false]], "__call__() (reorderafter method)": [[57, "cycquery.ops.ReorderAfter.__call__", false]], "__call__() (sequential method)": [[58, "cycquery.ops.Sequential.__call__", false]], "__call__() (substring method)": [[59, "cycquery.ops.Substring.__call__", false]], "__call__() (trim method)": [[60, "cycquery.ops.Trim.__call__", false]], "__call__() (union method)": [[61, "cycquery.ops.Union.__call__", false]], "__init__() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.__init__", false]], "__init__() (sequential method)": [[58, "cycquery.ops.Sequential.__init__", false]], "addcolumn (class in cycquery.ops)": [[19, "cycquery.ops.AddColumn", false]], "adddeltacolumn (class in cycquery.ops)": [[20, "cycquery.ops.AddDeltaColumn", false]], "adddeltaconstant (class in cycquery.ops)": [[21, "cycquery.ops.AddDeltaConstant", false]], "addnumeric (class in cycquery.ops)": [[22, "cycquery.ops.AddNumeric", false]], "and (class in cycquery.ops)": [[23, "cycquery.ops.And", false]], "append() (sequential method)": [[58, "cycquery.ops.Sequential.append", false]], "apply (class in cycquery.ops)": [[24, "cycquery.ops.Apply", false]], "care_units() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.care_units", false]], "cast (class in cycquery.ops)": [[25, "cycquery.ops.Cast", false]], "chartevents() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.chartevents", false]], "chartevents() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.chartevents", false]], "clear_data() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.clear_data", false]], "conditionafterdate (class in cycquery.ops)": [[26, "cycquery.ops.ConditionAfterDate", false]], "conditionbeforedate (class in cycquery.ops)": [[27, "cycquery.ops.ConditionBeforeDate", false]], "conditionendswith (class in cycquery.ops)": [[28, "cycquery.ops.ConditionEndsWith", false]], "conditionequals (class in cycquery.ops)": [[29, "cycquery.ops.ConditionEquals", false]], "conditiongreaterthan (class in cycquery.ops)": [[30, "cycquery.ops.ConditionGreaterThan", false]], "conditionin (class in cycquery.ops)": [[31, "cycquery.ops.ConditionIn", false]], "conditioninmonths (class in cycquery.ops)": [[32, "cycquery.ops.ConditionInMonths", false]], "conditioninyears (class in cycquery.ops)": [[33, "cycquery.ops.ConditionInYears", false]], "conditionlessthan (class in cycquery.ops)": [[34, "cycquery.ops.ConditionLessThan", false]], "conditionlike (class in cycquery.ops)": [[35, "cycquery.ops.ConditionLike", false]], "conditionregexmatch (class in cycquery.ops)": [[36, "cycquery.ops.ConditionRegexMatch", false]], "conditionstartswith (class in cycquery.ops)": [[37, "cycquery.ops.ConditionStartsWith", false]], "conditionsubstring (class in cycquery.ops)": [[38, "cycquery.ops.ConditionSubstring", false]], "count (class in cycquery.ops)": [[39, "cycquery.ops.Count", false]], "cycquery": [[62, "module-cycquery", false]], "cycquery.base": [[4, "module-cycquery.base", false]], "cycquery.eicu": [[6, "module-cycquery.eicu", false]], "cycquery.gemini": [[8, "module-cycquery.gemini", false]], "cycquery.interface": [[10, "module-cycquery.interface", false]], "cycquery.mimiciii": [[12, "module-cycquery.mimiciii", false]], "cycquery.mimiciv": [[14, "module-cycquery.mimiciv", false]], "cycquery.omop": [[16, "module-cycquery.omop", false]], "cycquery.ops": [[18, "module-cycquery.ops", false]], "data (queryinterface property)": [[11, "cycquery.interface.QueryInterface.data", false]], "datasetquerier (class in cycquery.base)": [[5, "cycquery.base.DatasetQuerier", false]], "db (datasetquerier attribute)": [[5, "cycquery.base.DatasetQuerier.db", false]], "diagnoses() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.diagnoses", false]], "diagnoses() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.diagnoses", false]], "diagnoses_icd() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.diagnoses_icd", false]], "distinct (class in cycquery.ops)": [[40, "cycquery.ops.Distinct", false]], "drop (class in cycquery.ops)": [[41, "cycquery.ops.Drop", false]], "dropempty (class in cycquery.ops)": [[42, "cycquery.ops.DropEmpty", false]], "dropnulls (class in cycquery.ops)": [[43, "cycquery.ops.DropNulls", false]], "eicuquerier (class in cycquery.eicu)": [[7, "cycquery.eicu.EICUQuerier", false]], "extend() (sequential method)": [[58, "cycquery.ops.Sequential.extend", false]], "extracttimestampcomponent (class in cycquery.ops)": [[44, "cycquery.ops.ExtractTimestampComponent", false]], "fillnull (class in cycquery.ops)": [[45, "cycquery.ops.FillNull", false]], "geminiquerier (class in cycquery.gemini)": [[9, "cycquery.gemini.GEMINIQuerier", false]], "get_table() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.get_table", false]], "get_table() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.get_table", false]], "get_table() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.get_table", false]], "get_table() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.get_table", false]], "get_table() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.get_table", false]], "get_table() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.get_table", false]], "groupbyaggregate (class in cycquery.ops)": [[46, "cycquery.ops.GroupByAggregate", false]], "imaging() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.imaging", false]], "insert() (sequential method)": [[58, "cycquery.ops.Sequential.insert", false]], "ip_admin() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.ip_admin", false]], "join (class in cycquery.ops)": [[47, "cycquery.ops.Join", false]], "join() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.join", false]], "keep (class in cycquery.ops)": [[48, "cycquery.ops.Keep", false]], "labevents() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.labevents", false]], "labevents() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.labevents", false]], "limit (class in cycquery.ops)": [[49, "cycquery.ops.Limit", false]], "list_columns() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_columns", false]], "list_columns() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_columns", false]], "list_columns() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_columns", false]], "list_columns() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_columns", false]], "list_columns() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_columns", false]], "list_columns() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_columns", false]], "list_custom_tables() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_custom_tables", false]], "list_custom_tables() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_custom_tables", false]], "list_custom_tables() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_custom_tables", false]], "list_custom_tables() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_custom_tables", false]], "list_custom_tables() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_custom_tables", false]], "list_custom_tables() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_custom_tables", false]], "list_schemas() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_schemas", false]], "list_schemas() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_schemas", false]], "list_schemas() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_schemas", false]], "list_schemas() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_schemas", false]], "list_schemas() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_schemas", false]], "list_schemas() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_schemas", false]], "list_tables() (datasetquerier method)": [[5, "cycquery.base.DatasetQuerier.list_tables", false]], "list_tables() (eicuquerier method)": [[7, "cycquery.eicu.EICUQuerier.list_tables", false]], "list_tables() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.list_tables", false]], "list_tables() (mimiciiiquerier method)": [[13, "cycquery.mimiciii.MIMICIIIQuerier.list_tables", false]], "list_tables() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.list_tables", false]], "list_tables() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.list_tables", false]], "literal (class in cycquery.ops)": [[50, "cycquery.ops.Literal", false]], "map_concept_ids_to_name() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.map_concept_ids_to_name", false]], "measurement() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.measurement", false]], "mimiciiiquerier (class in cycquery.mimiciii)": [[13, "cycquery.mimiciii.MIMICIIIQuerier", false]], "mimicivquerier (class in cycquery.mimiciv)": [[15, "cycquery.mimiciv.MIMICIVQuerier", false]], "module": [[4, "module-cycquery.base", false], [6, "module-cycquery.eicu", false], [8, "module-cycquery.gemini", false], [10, "module-cycquery.interface", false], [12, "module-cycquery.mimiciii", false], [14, "module-cycquery.mimiciv", false], [16, "module-cycquery.omop", false], [18, "module-cycquery.ops", false], [62, "module-cycquery", false]], "observation() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.observation", false]], "omopquerier (class in cycquery.omop)": [[17, "cycquery.omop.OMOPQuerier", false]], "ops() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.ops", false]], "or (class in cycquery.ops)": [[51, "cycquery.ops.Or", false]], "orderby (class in cycquery.ops)": [[52, "cycquery.ops.OrderBy", false]], "patients() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.patients", false]], "person() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.person", false]], "pop() (sequential method)": [[58, "cycquery.ops.Sequential.pop", false]], "procedures_icd() (mimicivquerier method)": [[15, "cycquery.mimiciv.MIMICIVQuerier.procedures_icd", false]], "queryinterface (class in cycquery.interface)": [[11, "cycquery.interface.QueryInterface", false]], "queryop (class in cycquery.ops)": [[53, "cycquery.ops.QueryOp", false]], "randomizeorder (class in cycquery.ops)": [[54, "cycquery.ops.RandomizeOrder", false]], "rename (class in cycquery.ops)": [[55, "cycquery.ops.Rename", false]], "reorder (class in cycquery.ops)": [[56, "cycquery.ops.Reorder", false]], "reorderafter (class in cycquery.ops)": [[57, "cycquery.ops.ReorderAfter", false]], "room_transfer() (geminiquerier method)": [[9, "cycquery.gemini.GEMINIQuerier.room_transfer", false]], "run() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.run", false]], "save() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.save", false]], "sequential (class in cycquery.ops)": [[58, "cycquery.ops.Sequential", false]], "substring (class in cycquery.ops)": [[59, "cycquery.ops.Substring", false]], "trim (class in cycquery.ops)": [[60, "cycquery.ops.Trim", false]], "union (class in cycquery.ops)": [[61, "cycquery.ops.Union", false]], "union() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.union", false]], "union_all() (queryinterface method)": [[11, "cycquery.interface.QueryInterface.union_all", false]], "visit_detail() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.visit_detail", false]], "visit_occurrence() (omopquerier method)": [[17, "cycquery.omop.OMOPQuerier.visit_occurrence", false]]}, "objects": {"": [[62, 0, 0, "-", "cycquery"]], "cycquery": [[4, 0, 0, "-", "base"], [6, 0, 0, "-", "eicu"], [8, 0, 0, "-", "gemini"], [10, 0, 0, "-", "interface"], [12, 0, 0, "-", "mimiciii"], [14, 0, 0, "-", "mimiciv"], [16, 0, 0, "-", "omop"], [18, 0, 0, "-", "ops"]], "cycquery.base": [[5, 1, 1, "", "DatasetQuerier"]], "cycquery.base.DatasetQuerier": [[5, 2, 1, "", "db"], [5, 3, 1, "", "get_table"], [5, 3, 1, "", "list_columns"], [5, 3, 1, "", "list_custom_tables"], [5, 3, 1, "", "list_schemas"], [5, 3, 1, "", "list_tables"]], "cycquery.eicu": [[7, 1, 1, "", "EICUQuerier"]], "cycquery.eicu.EICUQuerier": [[7, 3, 1, "", "get_table"], [7, 3, 1, "", "list_columns"], [7, 3, 1, "", "list_custom_tables"], [7, 3, 1, "", "list_schemas"], [7, 3, 1, "", "list_tables"]], "cycquery.gemini": [[9, 1, 1, "", "GEMINIQuerier"]], "cycquery.gemini.GEMINIQuerier": [[9, 3, 1, "", "care_units"], [9, 3, 1, "", "diagnoses"], [9, 3, 1, "", "get_table"], [9, 3, 1, "", "imaging"], [9, 3, 1, "", "ip_admin"], [9, 3, 1, "", "list_columns"], [9, 3, 1, "", "list_custom_tables"], [9, 3, 1, "", "list_schemas"], [9, 3, 1, "", "list_tables"], [9, 3, 1, "", "room_transfer"]], "cycquery.interface": [[11, 1, 1, "", "QueryInterface"]], "cycquery.interface.QueryInterface": [[11, 3, 1, "", "__init__"], [11, 3, 1, "", "clear_data"], [11, 4, 1, "", "data"], [11, 3, 1, "", "join"], [11, 3, 1, "", "ops"], [11, 3, 1, "", "run"], [11, 3, 1, "", "save"], [11, 3, 1, "", "union"], [11, 3, 1, "", "union_all"]], "cycquery.mimiciii": [[13, 1, 1, "", "MIMICIIIQuerier"]], "cycquery.mimiciii.MIMICIIIQuerier": [[13, 3, 1, "", "chartevents"], [13, 3, 1, "", "diagnoses"], [13, 3, 1, "", "get_table"], [13, 3, 1, "", "labevents"], [13, 3, 1, "", "list_columns"], [13, 3, 1, "", "list_custom_tables"], [13, 3, 1, "", "list_schemas"], [13, 3, 1, "", "list_tables"]], "cycquery.mimiciv": [[15, 1, 1, "", "MIMICIVQuerier"]], "cycquery.mimiciv.MIMICIVQuerier": [[15, 3, 1, "", "chartevents"], [15, 3, 1, "", "diagnoses_icd"], [15, 3, 1, "", "get_table"], [15, 3, 1, "", "labevents"], [15, 3, 1, "", "list_columns"], [15, 3, 1, "", "list_custom_tables"], [15, 3, 1, "", "list_schemas"], [15, 3, 1, "", "list_tables"], [15, 3, 1, "", "patients"], [15, 3, 1, "", "procedures_icd"]], "cycquery.omop": [[17, 1, 1, "", "OMOPQuerier"]], "cycquery.omop.OMOPQuerier": [[17, 3, 1, "", "get_table"], [17, 3, 1, "", "list_columns"], [17, 3, 1, "", "list_custom_tables"], [17, 3, 1, "", "list_schemas"], [17, 3, 1, "", "list_tables"], [17, 3, 1, "", "map_concept_ids_to_name"], [17, 3, 1, "", "measurement"], [17, 3, 1, "", "observation"], [17, 3, 1, "", "person"], [17, 3, 1, "", "visit_detail"], [17, 3, 1, "", "visit_occurrence"]], "cycquery.ops": [[19, 1, 1, "", "AddColumn"], [20, 1, 1, "", "AddDeltaColumn"], [21, 1, 1, "", "AddDeltaConstant"], [22, 1, 1, "", "AddNumeric"], [23, 1, 1, "", "And"], [24, 1, 1, "", "Apply"], [25, 1, 1, "", "Cast"], [26, 1, 1, "", "ConditionAfterDate"], [27, 1, 1, "", "ConditionBeforeDate"], [28, 1, 1, "", "ConditionEndsWith"], [29, 1, 1, "", "ConditionEquals"], [30, 1, 1, "", "ConditionGreaterThan"], [31, 1, 1, "", "ConditionIn"], [32, 1, 1, "", "ConditionInMonths"], [33, 1, 1, "", "ConditionInYears"], [34, 1, 1, "", "ConditionLessThan"], [35, 1, 1, "", "ConditionLike"], [36, 1, 1, "", "ConditionRegexMatch"], [37, 1, 1, "", "ConditionStartsWith"], [38, 1, 1, "", "ConditionSubstring"], [39, 1, 1, "", "Count"], [40, 1, 1, "", "Distinct"], [41, 1, 1, "", "Drop"], [42, 1, 1, "", "DropEmpty"], [43, 1, 1, "", "DropNulls"], [44, 1, 1, "", "ExtractTimestampComponent"], [45, 1, 1, "", "FillNull"], [46, 1, 1, "", "GroupByAggregate"], [47, 1, 1, "", "Join"], [48, 1, 1, "", "Keep"], [49, 1, 1, "", "Limit"], [50, 1, 1, "", "Literal"], [51, 1, 1, "", "Or"], [52, 1, 1, "", "OrderBy"], [53, 1, 1, "", "QueryOp"], [54, 1, 1, "", "RandomizeOrder"], [55, 1, 1, "", "Rename"], [56, 1, 1, "", "Reorder"], [57, 1, 1, "", "ReorderAfter"], [58, 1, 1, "", "Sequential"], [59, 1, 1, "", "Substring"], [60, 1, 1, "", "Trim"], [61, 1, 1, "", "Union"]], "cycquery.ops.AddColumn": [[19, 3, 1, "", "__call__"]], "cycquery.ops.AddDeltaColumn": [[20, 3, 1, "", "__call__"]], "cycquery.ops.AddDeltaConstant": [[21, 3, 1, "", "__call__"]], "cycquery.ops.AddNumeric": [[22, 3, 1, "", "__call__"]], "cycquery.ops.And": [[23, 3, 1, "", "__call__"]], "cycquery.ops.Apply": [[24, 3, 1, "", "__call__"]], "cycquery.ops.Cast": [[25, 3, 1, "", "__call__"]], "cycquery.ops.ConditionAfterDate": [[26, 3, 1, "", "__call__"]], "cycquery.ops.ConditionBeforeDate": [[27, 3, 1, "", "__call__"]], "cycquery.ops.ConditionEndsWith": [[28, 3, 1, "", "__call__"]], "cycquery.ops.ConditionEquals": [[29, 3, 1, "", "__call__"]], "cycquery.ops.ConditionGreaterThan": [[30, 3, 1, "", "__call__"]], "cycquery.ops.ConditionIn": [[31, 3, 1, "", "__call__"]], "cycquery.ops.ConditionInMonths": [[32, 3, 1, "", "__call__"]], "cycquery.ops.ConditionInYears": [[33, 3, 1, "", "__call__"]], "cycquery.ops.ConditionLessThan": [[34, 3, 1, "", "__call__"]], "cycquery.ops.ConditionLike": [[35, 3, 1, "", "__call__"]], "cycquery.ops.ConditionRegexMatch": [[36, 3, 1, "", "__call__"]], "cycquery.ops.ConditionStartsWith": [[37, 3, 1, "", "__call__"]], "cycquery.ops.ConditionSubstring": [[38, 3, 1, "", "__call__"]], "cycquery.ops.Count": [[39, 3, 1, "", "__call__"]], "cycquery.ops.Distinct": [[40, 3, 1, "", "__call__"]], "cycquery.ops.Drop": [[41, 3, 1, "", "__call__"]], "cycquery.ops.DropEmpty": [[42, 3, 1, "", "__call__"]], "cycquery.ops.DropNulls": [[43, 3, 1, "", "__call__"]], "cycquery.ops.ExtractTimestampComponent": [[44, 3, 1, "", "__call__"]], "cycquery.ops.FillNull": [[45, 3, 1, "", "__call__"]], "cycquery.ops.GroupByAggregate": [[46, 3, 1, "", "__call__"]], "cycquery.ops.Join": [[47, 3, 1, "", "__call__"]], "cycquery.ops.Keep": [[48, 3, 1, "", "__call__"]], "cycquery.ops.Limit": [[49, 3, 1, "", "__call__"]], "cycquery.ops.Literal": [[50, 3, 1, "", "__call__"]], "cycquery.ops.Or": [[51, 3, 1, "", "__call__"]], "cycquery.ops.OrderBy": [[52, 3, 1, "", "__call__"]], "cycquery.ops.QueryOp": [[53, 3, 1, "", "__call__"]], "cycquery.ops.RandomizeOrder": [[54, 3, 1, "", "__call__"]], "cycquery.ops.Rename": [[55, 3, 1, "", "__call__"]], "cycquery.ops.Reorder": [[56, 3, 1, "", "__call__"]], "cycquery.ops.ReorderAfter": [[57, 3, 1, "", "__call__"]], "cycquery.ops.Sequential": [[58, 3, 1, "", "__add__"], [58, 3, 1, "", "__call__"], [58, 3, 1, "", "__init__"], [58, 3, 1, "", "append"], [58, 3, 1, "", "extend"], [58, 3, 1, "", "insert"], [58, 3, 1, "", "pop"]], "cycquery.ops.Substring": [[59, 3, 1, "", "__call__"]], "cycquery.ops.Trim": [[60, 3, 1, "", "__call__"]], "cycquery.ops.Union": [[61, 3, 1, "", "__call__"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "attribute", "Python attribute"], "3": ["py", "method", "Python method"], "4": ["py", "property", "Python property"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:attribute", "3": "py:method", "4": "py:property"}, "terms": {"": [5, 11, 17, 24, 45, 64, 65, 66, 67, 68], "0": [14, 45, 59, 64, 65, 66, 67, 68], "01": [26, 27, 65, 67, 68], "013066": 67, "02": 67, "027628": 68, "03": [64, 65, 66], "04": [64, 65], "043": 68, "047307": 67, "05": [64, 65], "07": [64, 67], "072297": 67, "079": 67, "08": 64, "088": 66, "09": [64, 65, 66, 67, 68], "090": 66, "093352": 65, "098": 64, "099": 64, "1": [3, 11, 21, 22, 24, 26, 27, 29, 30, 31, 32, 34, 45, 50, 63], "10": [49, 63, 64, 66, 68], "100": [63, 66, 67, 68], "1000": 67, "1000000": 11, "101": 63, "11": 68, "117": 67, "119": 67, "12": 68, "13": 67, "130": 67, "137625": 68, "145693": 65, "15": 68, "150477": 68, "156461": 64, "17": [64, 65, 66, 67, 68], "184133": 66, "189734": 65, "19": [65, 66, 67], "195": 66, "1a": 63, "1b": 63, "1c": 63, "2": [3, 14, 22, 24, 31, 32, 59, 63, 65], "20": [63, 67], "2009": 63, "201": 64, "2010": 63, "2011": 68, "2012": 68, "2013": 68, "2014": [63, 68], "2015": [63, 68], "2016": [63, 68], "2017": 68, "2018": 68, "2019": [33, 68], "2020": [26, 27, 33, 63], "2021": [63, 68], "2022": 68, "2023": [65, 68], "2024": [64, 66, 67, 68], "203": 64, "209": 68, "21": [65, 68], "219430": 67, "22": [66, 67, 68], "220583": 64, "229596": 66, "23": 67, "24": 67, "247521": 66, "248": 68, "249": 68, "25": 67, "26": 65, "263": 68, "265080": 64, "27": [66, 68], "28": 66, "281": 64, "2a": 63, "3": [63, 65, 68], "31": 63, "32": [66, 68], "32567": 65, "33": 68, "35": 68, "352773": 67, "382": 66, "383": 66, "39": [64, 65, 66, 67, 68], "4": [63, 65, 68], "401": [64, 67], "403": [64, 67], "42": 68, "425": 67, "427": 67, "434": 68, "436": 68, "449": 65, "45": [65, 67], "452071": 68, "461": 67, "462": 67, "482": 66, "484": 66, "49": [67, 68], "5": [63, 64, 65, 66, 68], "506": 65, "509553": 67, "51": 65, "52": [65, 68], "5432": [3, 17, 64, 66, 67, 68], "552542": 66, "58": 67, "5815": 68, "591": 65, "592": 65, "6": [63, 65, 66, 68], "601747": 64, "610": 67, "612": 67, "631": 66, "633": 66, "675141": 65, "689": 67, "691": 67, "692": 67, "694": 67, "7": [63, 65, 68], "719": 68, "719482": 67, "721": 68, "8": [63, 68], "814": 65, "815": 65, "82": 67, "820": 68, "822": 68, "833": 64, "835": 64, "839": 67, "841": 67, "856": 65, "857": 65, "9": 63, "902": 65, "903": 65, "9305": 65, "939296": 65, "955": 66, "986367": 67, "999": 67, "A": [10, 11, 21, 26, 27, 47], "And": [0, 67], "For": [1, 17], "If": [1, 17, 19, 20, 21, 22, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 52, 60], "In": 3, "It": [3, 24, 63], "No": [11, 68], "Not": 5, "OR": 51, "Or": 0, "The": [1, 3, 5, 11, 15, 20, 24, 48, 62, 63, 64, 66, 67, 68], "To": 1, "__add__": [0, 58], "__call__": [0, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "__init__": [0, 11, 58], "aado2": 63, "abov": 63, "abstract": 53, "accord": [17, 64, 66, 67, 68], "accordingli": [64, 66, 67, 68], "activ": 3, "ad": [11, 19, 20, 21, 22, 58], "add": [19, 20, 21, 22, 50, 58], "add_to": [19, 20, 21, 22], "addcolumn": 0, "adddeltacolumn": [0, 67], "adddeltaconst": 0, "addnumer": 0, "address": 5, "adjust": 15, "admdad": 65, "admiss": [63, 66], "admissiondrug": 64, "admissiondx": 64, "admittim": 67, "admitting_concept_id": 68, "advanc": 63, "after": [5, 15, 24, 26, 57, 58, 63], "aggfunc": 46, "aggreg": [3, 46], "aggsep": 46, "all": [1, 3, 11, 38, 52, 55, 61, 63, 65], "all_visit": 68, "allergi": 64, "allow": [5, 7, 9, 13, 15, 17, 63], "along": 1, "also": 24, "ampicillin": 68, "an": [1, 9, 11, 13, 15, 17, 20, 23, 47, 51, 55], "analysi": 1, "analyz": 54, "anchor_year": 15, "anchor_year_differ": 67, "anchor_year_group": 15, "ani": [11, 20, 28, 29, 30, 31, 34, 37, 38, 45, 50], "anoth": [11, 47, 55, 58], "any_": 38, "apacheapsvar": 64, "apachepatientresult": 64, "apachepredvar": 64, "api": [2, 3, 5, 7, 9, 13, 15, 16, 17, 63], "append": [0, 58], "appli": [0, 1, 15, 19, 20, 21, 22, 60], "approx": 63, "approxim": 15, "apr": 63, "april": 63, "ar": [5, 15, 24, 47], "arg": [53, 54, 58], "argument": [20, 28, 29, 30, 31, 34, 37, 38], "around": [3, 63], "ascend": [52, 65], "assign": 17, "assign_all_visit_id": 68, "assum": [24, 64, 66, 67, 68], "attent": 19, "attribut": 11, "autolog": 68, "automat": 5, "b": 38, "backend": 11, "bacteria": 68, "base": [0, 3, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "batch": [11, 63], "batch_mod": [11, 67], "batch_siz": [11, 67], "becom": [11, 54], "befor": [1, 27, 47], "being": [19, 20, 21, 22, 26, 27, 29, 32, 33], "between": 63, "bin": 3, "binarize_col": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "binaryexpress": [11, 47], "black": 1, "blood": 68, "bool": [5, 7, 9, 11, 13, 15, 17, 19, 20, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 52, 55, 61], "boolean": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "both": 47, "build": [5, 63], "built": 3, "ca": 65, "call": 53, "callabl": 24, "can": [1, 3, 5, 7, 9, 13, 15, 17, 24, 38], "cannot": 54, "care": [9, 15], "care_sit": 68, "care_unit": [0, 9], "careplancareprovid": 64, "careplaneol": 64, "careplangener": 64, "careplango": 64, "careplaninfectiousdiseas": 64, "carevu": 63, "cartesian": 47, "cast": [0, 5, 7, 9, 11, 13, 15, 17, 65, 67], "cast_timestamp_col": [5, 7, 9, 13, 15, 17], "categori": 67, "cd": 3, "cdm_sourc": 68, "cdm_synthea10": 68, "cefazolin": 68, "cefepim": 68, "ceftazidim": 68, "ceftriaxon": 68, "cefuroxim": 68, "certain": 54, "chain": [11, 58], "chart": [15, 63], "chart_ev": [66, 67], "chartev": [0, 13, 15, 66, 67], "chartevents_op": 66, "check": [1, 55], "check_exist": 55, "chronic": 63, "ciprofloxacin": 68, "class": [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62], "clear": 11, "clear_data": [0, 11], "code": [2, 64, 66, 67, 68], "codestyl": 3, "cohort": 68, "cohort_definit": 68, "col": [19, 24, 25, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 48, 50, 52, 56, 57, 59, 60], "col1": [3, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 41, 42, 43, 44, 45, 47, 48, 50, 52, 55, 56, 57, 58, 59, 60], "col1_bool": [26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38], "col1_new": [24, 45, 55], "col1_plus_1": [21, 22], "col1_plus_col2": [19, 20], "col1_plus_col3": 19, "col1_substr": 59, "col1_trim": 60, "col2": [3, 19, 20, 21, 22, 24, 25, 41, 42, 43, 45, 47, 48, 52, 56, 57, 58, 60], "col2_new": [24, 45], "col2_plus_1": 22, "col2_plus_col3": 19, "col2_trim": 60, "col3": [3, 19, 20, 47, 57], "collection_date_tim": 65, "column": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 52, 55, 56, 57, 59, 60], "coma": 68, "combin": [19, 23, 51], "come": 57, "commit": 2, "common": 68, "commun": 63, "complet": 56, "compon": 44, "comput": 11, "concept": [17, 68], "concept_ancestor": 68, "concept_class": 68, "concept_relationship": 68, "concept_synonym": 68, "cond": [11, 47], "cond_kwarg": [28, 29, 30, 31, 34, 37, 38], "cond_op": [23, 51], "condit": [3, 11, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 68], "condition_concept_id": 68, "condition_concept_nam": 68, "condition_era": 68, "condition_occurr": 68, "conditionafterd": [0, 65, 67, 68], "conditionbefored": [0, 65], "conditionendswith": 0, "conditionequ": [0, 64, 65, 66, 67], "conditiongreaterthan": 0, "conditionin": [0, 3, 23, 51], "conditioninmonth": 0, "conditioninyear": [0, 67], "conditionlessthan": [0, 66], "conditionlik": [0, 23, 51, 67], "conditionregexmatch": [0, 63], "conditionstartswith": 0, "conditionsubstr": [0, 3, 64, 65, 66, 67, 68], "config": [64, 66, 67, 68], "consid": 17, "construct": [9, 13, 15, 17, 20, 21], "contain": [11, 63], "contribut": 2, "convers": 25, "convert": [25, 47], "correspond": [17, 42, 43], "cost": 68, "count": [0, 46, 65, 68], "crd": [2, 6, 63], "creat": [3, 5, 11, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 60, 63], "csv": [11, 68], "cultur": 68, "current": 25, "custom": [5, 7, 9, 13, 15, 17, 66], "customlab": 64, "cycqueri": [0, 63, 64, 65, 66, 68], "d": 3, "dai": 21, "dask": 11, "data": [0, 3, 9, 11, 13, 15, 54, 67, 68], "databas": [2, 5, 7, 9, 10, 11, 13, 15, 17, 62, 63, 64, 65, 66, 67, 68], "dataclass": 11, "datafram": [3, 11], "dataset": [0, 5, 7, 9, 11, 13, 15, 17, 63], "datasetqueri": [0, 3, 7, 9, 13, 15, 17], "date": [25, 26, 27], "datetim": [5, 7, 9, 13, 15, 17, 21, 26, 27], "db": [0, 5, 65, 67], "dbm": [3, 5, 7, 9, 13, 15, 17, 64, 66, 67, 68], "dbname": 3, "dbsourc": 66, "dbtabl": [11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61], "dd": [26, 27], "death": 68, "default": [5, 11, 37], "defin": 11, "delirium_v4_0_1": 65, "delta": 21, "delta_kwarg": 20, "depend": 3, "derived_vari": 65, "descend": 52, "develop": 2, "device_exposur": 68, "df": 3, "di": 68, "diagnos": [0, 9, 13, 63], "diagnoses_icd": [0, 15, 67], "diagnoses_op": 67, "diagnosi": [9, 13, 15, 64], "diagnosisstr": 63, "dict": [46, 55], "dictionari": 46, "differ": [38, 47], "diffus": 68, "disabl": 24, "discharg": 63, "discharge_date_tim": 63, "discharge_to_concept_id": 68, "discharge_to_concept_nam": 68, "dischtim": 67, "disk": 68, "distinct": [0, 3, 65], "doc": 3, "docstr": 1, "dod": 15, "domain": 68, "don": 1, "dose_era": 68, "downstream": [5, 7, 9, 13, 15, 17], "drop": [0, 58], "dropempti": [0, 65], "dropnul": [0, 3], "drug_era": 68, "drug_exposur": 68, "drug_strength": 68, "drugnam": 64, "dst_col": 17, "dt": 68, "dtype": 68, "dtype_backend": 11, "e": [3, 5, 44, 47, 50], "e501": 24, "each": [17, 24, 52, 63, 64, 66, 67, 68], "ehr": [3, 5, 62, 63, 68], "eicu": [0, 2, 63], "eicu_crd": 64, "eicuqueri": [0, 63], "electron": 3, "empti": [5, 42], "encount": [9, 63], "encounters_lab": 65, "encounters_per_sit": 65, "encounters_queri": 65, "end": [28, 58, 63], "env": 3, "environ": [1, 3], "episod": 68, "episode_ev": 68, "equal": [29, 30, 34], "er": 65, "erdiagnosi": 65, "erintervent": 65, "error": 1, "etl": 68, "event": [15, 63], "exampl": [19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 63], "execut": [58, 64, 65, 66, 67, 68], "exist": [19, 20, 21, 22, 55, 60], "expens": 47, "expire_flag": 66, "express": 36, "extend": [0, 58], "extract": [44, 59, 64, 65, 66, 67, 68], "extract_str": 44, "extracttimestampcompon": 0, "f": [64, 65, 66, 67, 68], "fact_relationship": 68, "fals": [11, 19, 20, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 52, 61, 65], "femal": 63, "fetch": [9, 11], "fhir_etl": 67, "fhir_trm": 67, "file": [1, 5, 11], "file_format": 11, "fill": [1, 45], "fill_valu": 45, "fillnul": 0, "filter": [3, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 51, 63], "final": 58, "final_visit_id": 68, "finish": [64, 65, 66, 67, 68], "first": [61, 64, 66, 67, 68], "fix": 1, "flag": 47, "float": [22, 25], "follow": [57, 68], "forget": 1, "format": [1, 11, 26, 27, 47, 68], "framework": 11, "from": [3, 9, 11, 15, 17, 44, 47, 55, 60, 63, 64, 66, 68], "func": 24, "function": [15, 19, 20, 21, 22, 24, 46, 53, 60, 63, 64, 65, 66, 67, 68], "further": 1, "g": [3, 5, 44, 47, 50], "gastroenter": 63, "gemini": [0, 2, 63], "geminiqueri": [0, 63], "genc_id": 65, "gender": [64, 66, 67], "gender_concept_nam": 68, "gener": [11, 68], "gentamicin": 68, "get": [2, 5, 7, 9, 11, 13, 15, 17, 40, 59, 63], "get_tabl": [0, 5, 7, 9, 13, 15, 17], "given": [45, 58], "glasgow": 68, "glucos": 63, "googl": 1, "greater": [30, 34], "group": 46, "groupbi": 3, "groupby_col": 46, "groupbyaggreg": [0, 65], "guid": 1, "guidelin": [2, 3], "ha": 59, "hadm_id": [66, 67], "have": [5, 7, 9, 13, 15, 17, 31, 38, 47, 63], "hba1c": [23, 35, 51], "health": 3, "hemoglobin": 63, "henc": 3, "hint": 1, "hook": 2, "hospit": [15, 63], "hospital_num": 65, "hospitaldischargeyear": 64, "hospitalid": 64, "host": [3, 5, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "hous": 68, "how": [63, 64, 66, 67, 68], "hpc": 65, "html": 3, "i": [1, 3, 5, 11, 15, 17, 19, 20, 21, 22, 24, 38, 42, 43, 47, 54, 63, 64, 66, 67, 68], "icd": 63, "icd_vers": 67, "icu": 15, "id": 17, "identifi": 68, "iii": [2, 12, 13, 63, 68], "imag": [0, 9], "imipenem": 68, "implement": 53, "import": [3, 63], "includ": [3, 30, 34], "index": [11, 58, 59, 63], "index_col": [11, 67], "infecti": 63, "infer": 15, "info": [3, 9, 64, 65, 66, 67, 68], "inform": 44, "information_schema": [67, 68], "infusiondrug": 64, "initi": [11, 58], "input": 24, "insert": [0, 58], "instal": 2, "instanti": [5, 63], "instead": [23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 51], "instruct": [64, 66, 67, 68], "int": [5, 11, 22, 25, 32, 33, 47, 49, 58, 59], "int64": 68, "intakeoutput": 64, "integ": 50, "integr": 3, "intend": 5, "interest": 1, "interfac": [0, 9, 13, 15, 17], "interv": 20, "ip_admin": [0, 9], "ipdiagnosi": 65, "ipintervent": 65, "ipscu": 65, "isout": [11, 47, 68], "issu": 1, "iv": [2, 14, 63], "jane": [23, 51], "john": [23, 51], "join": [0, 3, 11, 15, 64, 65, 66, 67, 68], "join_tabl": [11, 47, 64, 66, 67, 68], "join_table_col": [11, 47], "just": 38, "kb": 68, "keep": [0, 47, 63], "kei": [46, 55, 58], "keyword": [28, 29, 30, 31, 34, 37, 38, 61, 63], "kwarg": [53, 54], "lab": [15, 63, 65], "lab_nam": [23, 35, 46, 51], "lab_name_agg": 46, "lab_name_bool": 35, "lab_op": 65, "label": [19, 20, 21, 22, 44, 46, 50, 60, 66, 67], "labev": [0, 13, 15, 66], "labnam": 64, "lambda": 24, "larg": 54, "last": 1, "later": 63, "least": 1, "left": 47, "len": [64, 65, 66, 67, 68], "less": [34, 63], "levofloxacin": 68, "like": [3, 17, 35], "limit": [0, 11, 54, 63, 66, 67, 68], "line": 24, "link": 1, "list": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 31, 32, 33, 38, 40, 41, 42, 43, 45, 46, 47, 48, 51, 52, 56, 57, 58, 60, 64, 65, 66, 67, 68], "list_column": [0, 5, 7, 9, 13, 15, 17], "list_custom_t": [0, 5, 7, 9, 13, 15, 17, 66], "list_schema": [0, 5, 7, 9, 13, 15, 17, 67, 68], "list_tabl": [0, 3, 5, 7, 9, 13, 15, 17, 64, 65, 68], "liter": [0, 11], "load": 68, "local": 3, "localhost": [3, 17, 64, 66, 67, 68], "locality_vari": 65, "locat": 68, "long": [24, 63], "long_titl": [66, 67], "lookup_cci": 65, "lookup_ccsr": 65, "lookup_diagnosi": 65, "lookup_er_administr": 65, "lookup_hospital_num": 65, "lookup_icd10_ca_descript": 65, "lookup_icd10_ca_to_ccsr": 65, "lookup_imag": 65, "lookup_ip_administr": 65, "lookup_ip_scu": 65, "lookup_lab_concept": 65, "lookup_pharmacy_concept": 65, "lookup_pharmacy_rout": 65, "lookup_phy_characterist": 65, "lookup_room_transf": 65, "lookup_statcan": 65, "lookup_transf": 65, "lookup_transfusion_concept": 65, "lookup_vitals_concept": 65, "lymphadenopathi": 63, "m": [3, 66], "mai": 63, "make": [3, 38], "male": 63, "manag": 5, "mani": [3, 63], "map": [5, 7, 9, 13, 15, 17, 55], "map_concept_ids_to_nam": [0, 17, 68], "march": 63, "match": [3, 36, 68], "measur": [0, 17, 63], "measurement_concept_nam": 68, "medic": 63, "meropenem": 68, "metadata": 68, "method": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 66], "microlab": 64, "million": 11, "mimic": [2, 12, 13, 14, 15, 63, 68], "mimic_fhir": 67, "mimiciii": [0, 66, 68], "mimiciiiqueri": [0, 63, 68], "mimiciv": [0, 67], "mimiciv_": 67, "mimiciv_deriv": 67, "mimiciv_hosp": 67, "mimiciv_icu": 67, "mimiciv_not": 67, "mimicivqueri": [0, 63], "mm": [26, 27], "mode": 11, "model": 68, "modul": [6, 8, 12, 14, 15], "month": [32, 44], "more": 3, "mortal": 63, "most": 63, "motor": 68, "multipl": [9, 23, 24, 46, 51], "must": [25, 31, 32, 33, 38, 46], "mypi": 1, "mysql": 5, "name": [5, 7, 9, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 51, 55, 56, 57, 59, 68], "nbsphinx_allow_error": 3, "need": [1, 59], "neg": [19, 20], "negat": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "neither": 47, "new": [19, 20, 21, 22, 24, 45, 46, 50, 56, 59, 60], "new_col": 24, "new_col_label": [19, 20, 21, 22, 59, 60], "new_col_nam": [45, 59], "next": 67, "nitrofurantoin": 68, "none": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 52, 59, 60], "noqa": 24, "nor": 47, "not_": [26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38], "note": [5, 15, 64, 68], "note_nlp": 68, "notebook": [64, 65, 66, 67, 68], "null": [43, 45], "number": [5, 39, 49, 57, 63], "numer": 22, "numpi": 1, "nurseassess": 64, "nursecar": 64, "nursechart": 64, "object": [5, 9, 10, 11, 13, 15, 17, 20, 21, 24, 26, 27, 46, 53, 58, 63], "observ": [0, 17, 68], "observation_period": 68, "occur": 63, "omop": [0, 2, 63], "omopqueri": [0, 63], "on_to_typ": [11, 47], "onc": 1, "one": [38, 63], "onli": [38, 47, 48, 63], "op": [0, 3, 11, 15, 63, 64, 65, 66, 68], "op_": 58, "oper": [3, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "oppos": 47, "option": [5, 7, 9, 11, 13, 15, 17, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 46, 47, 61], "order": [3, 11, 52, 54, 56, 57], "orderbi": [0, 65], "ordereddict": 58, "origin": 11, "orm": [5, 11, 63, 64, 65, 66, 67, 68], "other": [11, 19, 57, 58], "otherwis": [19, 20, 21, 22, 60], "our": 1, "out": 1, "outcom": 63, "outer": [11, 47], "over": 46, "pai": 19, "pair": 46, "panda": [3, 11, 68], "paramet": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 64, 66, 67, 68], "parenter": 68, "parquet": 11, "partit": [11, 63], "pass": [64, 66, 67, 68], "password": [3, 5, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "pasthistori": 64, "path": [3, 5, 11], "patient": [0, 9, 15, 63], "patient_admiss": [66, 67], "patient_admissions_df": 67, "patient_admissions_diagnos": [66, 67], "patient_admissions_lab": 67, "patient_admissions_radiology_not": 67, "patient_admissions_vit": 67, "patient_chart_ev": 66, "patient_diagnos": 64, "patient_id_hash": 63, "patient_lab": [64, 66], "patient_med": 64, "patientunitstayid": 64, "pattern": 35, "payer_plan_period": 68, "pd": 68, "per": 63, "perform": [3, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 68], "person": [0, 17, 68], "person_id": [39, 40, 46, 68], "person_visit": 68, "person_visits_condit": 68, "person_visits_conditions_measur": 68, "pharmaci": 65, "physicalexam": 64, "pip": 2, "piperacillin": 68, "place": 63, "pleas": 1, "poetri": 2, "pop": [0, 58], "port": [3, 5, 7, 9, 13, 15, 17, 64, 66, 67, 68], "possibli": [5, 7, 9, 13, 15, 17], "postgr": [64, 66, 67, 68], "postgresql": [2, 5, 17, 63, 64, 66, 67, 68], "potassium": 63, "pr": 1, "pre": 2, "prevent": 46, "print": [64, 65, 66, 67, 68], "procedur": 15, "procedure_occurr": 68, "procedures_icd": [0, 15], "process": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61], "product": [47, 68], "profil": [64, 65, 66, 67, 68], "properti": 11, "provid": [5, 7, 9, 13, 15, 17, 24, 38, 45, 46, 52, 62, 68], "public": [65, 67, 68], "pwd": [5, 64, 66, 67, 68], "pyarrow": [11, 68], "pylint": 24, "python": [1, 3, 63], "python3": 3, "qo": [3, 64, 65, 66, 67, 68], "queri": [2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 49, 51, 53, 58, 62, 63, 64, 65, 66, 67, 68], "querier": [3, 4, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "queryinterfac": [0, 9, 13, 15, 17], "queryop": [0, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61], "quick": [64, 66, 67, 68], "quit": 54, "r": 67, "radiologi": [63, 65], "radiology_not": 67, "radiology_notes_op": 67, "random": 54, "randomizeord": 0, "rate": 68, "rather": [19, 20], "raw": 63, "readi": [64, 65, 66, 67, 68], "receiv": 15, "recent": 63, "recogn": [5, 7, 9, 13, 15, 17], "recommend": 1, "record": [3, 63], "refer": 2, "regex": 36, "regular": 36, "relat": 3, "relationship": 68, "releas": 68, "remov": [42, 43], "renam": 0, "rename_map": 55, "reorder": [0, 57], "reorderaft": 0, "repo": 68, "report": [9, 63], "repres": 47, "respiratori": 68, "respiratorycar": 64, "respiratorychart": 64, "result": [11, 58, 64, 66, 67, 68], "return": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 65, 66, 68], "return_cond": [23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 51], "room": 9, "room_transf": [0, 9], "roomtransf": 65, "routin": 63, "row": [11, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 49, 52, 54, 63, 65, 66, 67, 68], "ruff": 1, "run": [0, 1, 3, 5, 11, 63, 64, 65, 66, 68], "run_queri": [64, 65, 66, 67, 68], "sai": 47, "same": [46, 47], "save": [0, 11], "schema": [3, 5, 7, 9, 13, 15, 17, 67, 68], "schema_nam": [5, 7, 9, 13, 15, 17, 68], "schizophrenia": 63, "score": 68, "search": 63, "see": 3, "seen": 54, "select": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 67], "self": 5, "separ": 46, "sepsi": 63, "sequenc": [46, 58], "sequenti": [0, 3, 11, 64, 65, 66, 67, 68], "server": 11, "set": [3, 11, 63], "setup": [1, 64, 65, 66, 67, 68], "should": 11, "show": [1, 64, 65, 66, 67, 68], "showcas": 68, "sign": 63, "simpl": 3, "singl": 24, "size": 11, "slice": 58, "slow": 54, "so": 54, "sodium": 63, "sodium_test": 65, "some": [3, 19, 20, 21, 22, 26, 27, 28, 29, 30, 34, 37, 41, 42, 43, 52, 55, 60], "somecol_concept_id": 17, "somecol_concept_nam": 17, "somet": 3, "sort": [52, 63], "sort_index": 68, "sourc": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "source_to_concept_map": 68, "source_to_source_vocab_map": 68, "source_to_standard_vocab_map": 68, "specif": 3, "specifi": [17, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 46, 47, 48, 57, 60], "specimen": 68, "sphinx": 3, "sphinxopt": 3, "sql": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 63], "sqlalchemi": [3, 5, 7, 9, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 63], "sqlite": 5, "src_col": 17, "src_tabl": 17, "standard": [5, 7, 9, 13, 15, 17], "start": [2, 37, 59], "start_index": 59, "static": 1, "stop": 59, "stop_index": 59, "str": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 52, 55, 56, 57, 58, 59, 60, 67], "string": [28, 37, 46, 47, 50, 59, 60, 63], "string_agg": 46, "string_aggfunc": 46, "style": [1, 47], "subclass": 5, "subject_id": [63, 66], "submit": 1, "subqueri": [5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "subset": 63, "substr": [0, 3, 38, 63], "subtract": [19, 20], "successfulli": [64, 65, 66, 67, 68], "suggest": 47, "sulbactam": 68, "sulfamethoxazol": 68, "suppli": 15, "support": [6, 12, 14, 25], "sure": 3, "suscept": 68, "synthea": 68, "synthea_integration_test": 68, "system": 5, "t": 1, "tabl": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 63, 64, 66, 68], "table1": [47, 61], "table2": [47, 61], "table_col": [11, 47], "table_nam": [5, 7, 9, 13, 15, 17], "take": [24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 63], "tazobactam": 68, "teach": 63, "teachingstatu": 64, "templat": 1, "test": [3, 63], "test_type_map": 65, "text": 67, "than": [19, 20, 30, 34, 63], "thank": 1, "them": 11, "thi": [5, 22, 38, 46, 47, 64, 65, 66, 67, 68], "thu": 11, "time": 44, "timedelta": 21, "timestamp": [5, 7, 9, 13, 15, 17, 25, 26, 27, 32, 33, 44, 65], "timestamp_col": [26, 27, 32, 33, 44], "titl": 63, "to_datetim": 68, "tobramycin": 68, "togeth": 63, "too": 24, "tool": [1, 3, 63, 64, 65, 66, 67, 68], "total": 63, "transfer": 9, "transfus": 65, "treatment": 64, "trim": 0, "trimethoprim": 68, "true": [3, 5, 7, 9, 11, 13, 15, 17, 19, 20, 35, 38, 52, 55, 61, 64, 65, 67, 68], "tupl": [11, 47], "tutori": 2, "two": [47, 58, 61], "type": [1, 5, 7, 9, 11, 13, 15, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61], "type_": 25, "union": [0, 5, 11, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60], "union_al": [0, 11, 61], "union_t": 61, "unit": [3, 9, 68], "up": 3, "updat": [64, 66, 67, 68], "upstream": 11, "urin": 68, "us": [1, 2, 5, 7, 9, 11, 13, 15, 17, 20, 23, 40, 46, 47, 51, 54, 61, 63, 64, 65, 66, 68], "usenam": 3, "user": [3, 5, 7, 9, 13, 15, 17, 64, 65, 66, 67, 68], "usernam": [5, 64, 65, 66, 67, 68], "util": [64, 65, 66, 67, 68], "v1": [66, 68], "v2": [67, 68], "valu": [22, 29, 30, 31, 34, 42, 43, 45, 46, 47, 50], "value_count": 68, "valuenum": 63, "virtual": 1, "visit": 63, "visit_count": 46, "visit_detail": [0, 17, 68], "visit_id": 40, "visit_occurr": [0, 17, 68], "visit_occurrence_id": 68, "visit_start_d": 68, "visits_concept_map": 68, "visits_concept_mapped_di": 68, "visits_measur": 68, "vital": [63, 65], "vitalaperiod": 64, "vitalperiod": 64, "vocabulari": 68, "we": [1, 68], "welcom": 3, "were": 63, "when": [5, 38, 47, 54], "where": [11, 59], "wherea": 19, "whether": [5, 7, 9, 11, 13, 15, 17, 38, 52, 55, 61], "which": [1, 5, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 59, 60, 61, 68], "whitespac": 60, "who": 63, "work": 19, "wrap": [9, 10, 11, 13, 15, 17], "wrapper": [3, 63], "write": 3, "x": 24, "y": 24, "year": [15, 32, 33, 44, 63, 68], "you": [1, 63], "your": 1, "yyyi": [26, 27]}, "titles": ["API Reference", "Contributing to cycquery", "Welcome to cycquery\u2019s documentation!", "cycquery", "cycquery.base", "cycquery.base.DatasetQuerier", "cycquery.eicu", "cycquery.eicu.EICUQuerier", "cycquery.gemini", "cycquery.gemini.GEMINIQuerier", "cycquery.interface", "cycquery.interface.QueryInterface", "cycquery.mimiciii", "cycquery.mimiciii.MIMICIIIQuerier", "cycquery.mimiciv", "cycquery.mimiciv.MIMICIVQuerier", "cycquery.omop", "cycquery.omop.OMOPQuerier", "cycquery.ops", "cycquery.ops.AddColumn", "cycquery.ops.AddDeltaColumn", "cycquery.ops.AddDeltaConstant", "cycquery.ops.AddNumeric", "cycquery.ops.And", "cycquery.ops.Apply", "cycquery.ops.Cast", "cycquery.ops.ConditionAfterDate", "cycquery.ops.ConditionBeforeDate", "cycquery.ops.ConditionEndsWith", "cycquery.ops.ConditionEquals", "cycquery.ops.ConditionGreaterThan", "cycquery.ops.ConditionIn", "cycquery.ops.ConditionInMonths", "cycquery.ops.ConditionInYears", "cycquery.ops.ConditionLessThan", "cycquery.ops.ConditionLike", "cycquery.ops.ConditionRegexMatch", "cycquery.ops.ConditionStartsWith", "cycquery.ops.ConditionSubstring", "cycquery.ops.Count", "cycquery.ops.Distinct", "cycquery.ops.Drop", "cycquery.ops.DropEmpty", "cycquery.ops.DropNulls", "cycquery.ops.ExtractTimestampComponent", "cycquery.ops.FillNull", "cycquery.ops.GroupByAggregate", "cycquery.ops.Join", "cycquery.ops.Keep", "cycquery.ops.Limit", "cycquery.ops.Literal", "cycquery.ops.Or", "cycquery.ops.OrderBy", "cycquery.ops.QueryOp", "cycquery.ops.RandomizeOrder", "cycquery.ops.Rename", "cycquery.ops.Reorder", "cycquery.ops.ReorderAfter", "cycquery.ops.Sequential", "cycquery.ops.Substring", "cycquery.ops.Trim", "cycquery.ops.Union", "cycquery", "Tutorials", "eICU-CRD tutorial", "GEMINI tutorial", "MIMIC-III tutorial", "MIMIC-IV tutorial", "OMOP tutorial"], "titleterms": {"": 2, "1": [64, 65, 66, 67, 68], "10": 67, "100": 64, "101": 65, "1a": 65, "1b": 65, "1c": 65, "2": [64, 66, 67, 68], "20": 66, "2009": 67, "2010": 68, "2014": 64, "2015": [64, 65, 67], "2016": 65, "2020": 68, "2021": 67, "2a": 65, "3": [64, 66, 67], "31": 65, "4": [64, 66, 67], "5": 67, "6": 67, "7": 67, "8": 67, "9": [66, 67], "And": 23, "Or": 51, "aado2": 66, "abov": 65, "addcolumn": 19, "adddeltacolumn": 20, "adddeltaconst": 21, "addnumer": 22, "admiss": [65, 67], "advanc": 67, "after": 68, "all": [64, 66, 67, 68], "api": [0, 62], "appli": 24, "approx": 67, "apr": 65, "april": 65, "base": [4, 5], "batch": 67, "between": 65, "carevu": 66, "cast": 25, "chart": 66, "chronic": 67, "code": 1, "commit": 1, "conditionafterd": 26, "conditionbefored": 27, "conditionendswith": 28, "conditionequ": 29, "conditiongreaterthan": 30, "conditionin": 31, "conditioninmonth": 32, "conditioninyear": 33, "conditionlessthan": 34, "conditionlik": 35, "conditionregexmatch": [36, 67], "conditionstartswith": 37, "conditionsubstr": 38, "contain": 67, "content": 2, "contribut": [1, 3], "count": 39, "crd": 64, "creat": 65, "cycqueri": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 67], "databas": 3, "dataset": [62, 65], "datasetqueri": 5, "develop": 3, "diagnos": [64, 66, 67, 68], "diagnosisstr": 64, "discharg": [64, 65], "discharge_date_tim": 65, "distinct": 40, "document": [2, 3], "drop": 41, "dropempti": 42, "dropnul": 43, "each": 65, "eicu": [6, 7, 64], "eicuqueri": [7, 64], "encount": [64, 65, 66, 67], "end": 68, "event": 66, "exampl": [64, 65, 66, 67, 68], "extracttimestampcompon": 44, "femal": [64, 66, 67, 68], "fillnul": 45, "filter": 67, "from": [65, 67], "gastroenter": 66, "gemini": [8, 9, 65], "geminiqueri": [9, 65], "get": [3, 64, 65, 66, 67, 68], "glucos": 64, "groupbyaggreg": 46, "guidelin": 1, "have": 66, "hemoglobin": 67, "hook": 1, "hospit": [64, 65], "how": 65, "icd": [66, 67], "iii": 66, "import": [64, 65, 66, 67, 68], "index": 67, "infecti": 67, "instal": 3, "instanti": [64, 65, 66, 67, 68], "interfac": [10, 11], "iv": 67, "join": 47, "keep": [48, 65], "keyword": 67, "lab": [64, 66, 67], "later": 67, "less": 66, "limit": [49, 64], "liter": 50, "long": [66, 67], "lymphadenopathi": 67, "mai": 65, "male": 66, "mani": 65, "march": 65, "measur": 68, "medic": 64, "mimic": [66, 67], "mimiciii": [12, 13], "mimiciiiqueri": [13, 66], "mimiciv": [14, 15], "mimicivqueri": [15, 67], "mortal": [66, 68], "most": 65, "number": 65, "occur": 67, "omop": [16, 17, 68], "omopqueri": [17, 68], "one": 65, "onli": 65, "op": [18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 67], "orderbi": 52, "outcom": [66, 68], "partit": 67, "patient": [64, 65, 66, 67, 68], "patient_id_hash": 65, "per": 65, "pip": 3, "place": 65, "poetri": 3, "postgresql": 3, "potassium": [64, 66], "pre": 1, "queri": 3, "queryinterfac": 11, "queryop": 53, "radiologi": 67, "randomizeord": 54, "raw": 67, "recent": 65, "record": 65, "refer": 0, "renam": 55, "reorder": 56, "reorderaft": 57, "report": 67, "return": 67, "routin": 67, "row": 64, "run": 67, "schizophrenia": [64, 67], "search": 64, "sepsi": 68, "sequenti": 58, "set": 65, "sign": 67, "sodium": 65, "sort": 65, "sql": 67, "start": 3, "string": 67, "subject_id": 67, "subset": 65, "substr": [59, 64], "tabl": 65, "take": 65, "teach": 64, "test": [64, 65, 66, 67], "than": 66, "titl": [66, 67], "togeth": 67, "total": 65, "trim": 60, "tutori": [63, 64, 65, 66, 67, 68], "union": 61, "us": [3, 67], "valuenum": 66, "visit": 68, "vital": 67, "welcom": 2, "were": 65, "who": 65, "year": [64, 67]}}) \ No newline at end of file diff --git a/tutorials/eicu.html b/tutorials/eicu.html index 3e1cfc9..fc5fad9 100644 --- a/tutorials/eicu.html +++ b/tutorials/eicu.html @@ -615,7 +615,7 @@
-2024-09-17 07:41:11,900 INFO cycquery.orm - Database setup, ready to run queries!
+2024-09-17 10:03:04,281 INFO cycquery.orm - Database setup, ready to run queries!
@@ -679,7 +679,7 @@ Example 1. Get all female patients discharged in 2014 (limit to 100 rows).
-2024-09-17 07:41:12,856 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:03:05,201 INFO cycquery.orm - Query returned successfully!
@@ -687,7 +687,7 @@ Example 1. Get all female patients discharged in 2014 (limit to 100 rows).
-2024-09-17 07:41:12,858 INFO cycquery.utils.profile - Finished executing function run_query in 0.183889 s
+2024-09-17 10:03:05,203 INFO cycquery.utils.profile - Finished executing function run_query in 0.156461 s
@@ -722,7 +722,7 @@ Example 2. Get all patient encounters with diagnoses (
-2024-09-17 07:41:15,369 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:03:07,833 INFO cycquery.orm - Query returned successfully!
@@ -730,7 +730,7 @@ Example 2. Get all patient encounters with diagnoses (
-2024-09-17 07:41:15,371 INFO cycquery.utils.profile - Finished executing function run_query in 2.483853 s
+2024-09-17 10:03:07,835 INFO cycquery.utils.profile - Finished executing function run_query in 2.601747 s
@@ -771,7 +771,7 @@ Example 3. Get potassium lab tests for patients discharged in the year 2014,
-2024-09-17 07:41:15,821 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:03:08,098 INFO cycquery.orm - Query returned successfully!
@@ -779,7 +779,7 @@ Example 3. Get potassium lab tests for patients discharged in the year 2014,
-2024-09-17 07:41:15,823 INFO cycquery.utils.profile - Finished executing function run_query in 0.407262 s
+2024-09-17 10:03:08,099 INFO cycquery.utils.profile - Finished executing function run_query in 0.220583 s
@@ -818,7 +818,7 @@ Example 4. Get glucose medications (substring search) for female patients di
-2024-09-17 07:41:21,962 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:03:09,401 INFO cycquery.orm - Query returned successfully!
@@ -826,7 +826,7 @@ Example 4. Get glucose medications (substring search) for female patients di
-2024-09-17 07:41:21,964 INFO cycquery.utils.profile - Finished executing function run_query in 6.101793 s
+2024-09-17 10:03:09,403 INFO cycquery.utils.profile - Finished executing function run_query in 1.265080 s
diff --git a/tutorials/eicu.ipynb b/tutorials/eicu.ipynb
index 1d3b36f..5447d53 100644
--- a/tutorials/eicu.ipynb
+++ b/tutorials/eicu.ipynb
@@ -35,10 +35,10 @@
"id": "75a140e0-fb27-4319-862f-be54397abe5c",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:41:09.842152Z",
- "iopub.status.busy": "2024-09-17T11:41:09.840879Z",
- "iopub.status.idle": "2024-09-17T11:41:12.653328Z",
- "shell.execute_reply": "2024-09-17T11:41:12.651500Z"
+ "iopub.execute_input": "2024-09-17T14:03:02.283750Z",
+ "iopub.status.busy": "2024-09-17T14:03:02.282786Z",
+ "iopub.status.idle": "2024-09-17T14:03:05.025269Z",
+ "shell.execute_reply": "2024-09-17T14:03:05.023548Z"
},
"tags": []
},
@@ -47,7 +47,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:11,900 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-09-17 10:03:04,281 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
]
},
{
@@ -124,10 +124,10 @@
"id": "c1efa964-8978-4a0e-9892-5ea4ce9953a3",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:41:12.661164Z",
- "iopub.status.busy": "2024-09-17T11:41:12.659623Z",
- "iopub.status.idle": "2024-09-17T11:41:12.865180Z",
- "shell.execute_reply": "2024-09-17T11:41:12.863532Z"
+ "iopub.execute_input": "2024-09-17T14:03:05.033431Z",
+ "iopub.status.busy": "2024-09-17T14:03:05.031939Z",
+ "iopub.status.idle": "2024-09-17T14:03:05.210453Z",
+ "shell.execute_reply": "2024-09-17T14:03:05.208794Z"
},
"tags": []
},
@@ -136,14 +136,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:12,856 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:03:05,201 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:12,858 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.183889 s\n"
+ "2024-09-17 10:03:05,203 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.156461 s\n"
]
},
{
@@ -180,10 +180,10 @@
"id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:41:12.872462Z",
- "iopub.status.busy": "2024-09-17T11:41:12.871370Z",
- "iopub.status.idle": "2024-09-17T11:41:15.379456Z",
- "shell.execute_reply": "2024-09-17T11:41:15.377666Z"
+ "iopub.execute_input": "2024-09-17T14:03:05.218060Z",
+ "iopub.status.busy": "2024-09-17T14:03:05.216811Z",
+ "iopub.status.idle": "2024-09-17T14:03:07.842113Z",
+ "shell.execute_reply": "2024-09-17T14:03:07.840483Z"
},
"tags": []
},
@@ -192,14 +192,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:15,369 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:03:07,833 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:15,371 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.483853 s\n"
+ "2024-09-17 10:03:07,835 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 2.601747 s\n"
]
},
{
@@ -236,10 +236,10 @@
"id": "24043abc-1878-4e00-8229-36d4a0368b98",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:41:15.386815Z",
- "iopub.status.busy": "2024-09-17T11:41:15.385758Z",
- "iopub.status.idle": "2024-09-17T11:41:15.830851Z",
- "shell.execute_reply": "2024-09-17T11:41:15.829168Z"
+ "iopub.execute_input": "2024-09-17T14:03:07.849876Z",
+ "iopub.status.busy": "2024-09-17T14:03:07.848529Z",
+ "iopub.status.idle": "2024-09-17T14:03:08.107187Z",
+ "shell.execute_reply": "2024-09-17T14:03:08.105505Z"
},
"tags": []
},
@@ -248,14 +248,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:15,821 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:03:08,098 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:15,823 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.407262 s\n"
+ "2024-09-17 10:03:08,099 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.220583 s\n"
]
},
{
@@ -298,10 +298,10 @@
"id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:41:15.838158Z",
- "iopub.status.busy": "2024-09-17T11:41:15.837113Z",
- "iopub.status.idle": "2024-09-17T11:41:21.971187Z",
- "shell.execute_reply": "2024-09-17T11:41:21.969559Z"
+ "iopub.execute_input": "2024-09-17T14:03:08.114384Z",
+ "iopub.status.busy": "2024-09-17T14:03:08.113374Z",
+ "iopub.status.idle": "2024-09-17T14:03:09.411649Z",
+ "shell.execute_reply": "2024-09-17T14:03:09.409692Z"
},
"tags": []
},
@@ -310,14 +310,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:21,962 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:03:09,401 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:21,964 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 6.101793 s\n"
+ "2024-09-17 10:03:09,403 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.265080 s\n"
]
},
{
diff --git a/tutorials/mimiciii.html b/tutorials/mimiciii.html
index d0e0730..0c9299f 100644
--- a/tutorials/mimiciii.html
+++ b/tutorials/mimiciii.html
@@ -615,7 +615,7 @@ Imports and instantiate
-2024-09-17 07:41:35,289 INFO cycquery.orm - Database setup, ready to run queries!
+2024-09-17 10:03:22,195 INFO cycquery.orm - Database setup, ready to run queries!
@@ -649,7 +649,7 @@ Example 1. Get all male patients with a mortality outcome.
-2024-09-17 07:41:41,641 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:03:28,482 INFO cycquery.orm - Query returned successfully!
@@ -657,7 +657,7 @@ Example 1. Get all male patients with a mortality outcome.
-2024-09-17 07:41:41,642 INFO cycquery.utils.profile - Finished executing function run_query in 0.180899 s
+2024-09-17 10:03:28,484 INFO cycquery.utils.profile - Finished executing function run_query in 0.229596 s
@@ -697,7 +697,7 @@ Example 2. Get all female patient encounters with diagnoses (
-2024-09-17 07:41:44,927 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:03:32,088 INFO cycquery.orm - Query returned successfully!
@@ -705,7 +705,7 @@ Example 2. Get all female patient encounters with diagnoses (
-2024-09-17 07:41:44,929 INFO cycquery.utils.profile - Finished executing function run_query in 3.234838 s
+2024-09-17 10:03:32,090 INFO cycquery.utils.profile - Finished executing function run_query in 3.552542 s
@@ -737,7 +737,7 @@ Example 3. Get potassium lab tests for female patients.
-2024-09-17 07:41:45,306 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:03:32,382 INFO cycquery.orm - Query returned successfully!
@@ -745,7 +745,7 @@ Example 3. Get potassium lab tests for female patients.
-2024-09-17 07:41:45,308 INFO cycquery.utils.profile - Finished executing function run_query in 0.330425 s
+2024-09-17 10:03:32,383 INFO cycquery.utils.profile - Finished executing function run_query in 0.247521 s
@@ -782,7 +782,7 @@ Example 4. Get AaDO2 carevue chart events for male patients that have a
-2024-09-17 07:57:34,936 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:19:27,631 INFO cycquery.orm - Query returned successfully!
@@ -790,7 +790,7 @@ Example 4. Get AaDO2 carevue chart events for male patients that have a
-2024-09-17 07:57:34,938 INFO cycquery.utils.profile - Finished executing function run_query in 949.564382 s
+2024-09-17 10:19:27,633 INFO cycquery.utils.profile - Finished executing function run_query in 955.184133 s
diff --git a/tutorials/mimiciii.ipynb b/tutorials/mimiciii.ipynb
index 6e9cfd8..a7d7a2d 100644
--- a/tutorials/mimiciii.ipynb
+++ b/tutorials/mimiciii.ipynb
@@ -35,10 +35,10 @@
"id": "75a140e0-fb27-4319-862f-be54397abe5c",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:41:27.746254Z",
- "iopub.status.busy": "2024-09-17T11:41:27.745208Z",
- "iopub.status.idle": "2024-09-17T11:41:41.445852Z",
- "shell.execute_reply": "2024-09-17T11:41:41.444040Z"
+ "iopub.execute_input": "2024-09-17T14:03:14.855205Z",
+ "iopub.status.busy": "2024-09-17T14:03:14.854331Z",
+ "iopub.status.idle": "2024-09-17T14:03:28.238189Z",
+ "shell.execute_reply": "2024-09-17T14:03:28.236347Z"
},
"tags": []
},
@@ -47,7 +47,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:35,289 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-09-17 10:03:22,195 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
]
},
{
@@ -94,10 +94,10 @@
"id": "c1efa964-8978-4a0e-9892-5ea4ce9953a3",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:41:41.453783Z",
- "iopub.status.busy": "2024-09-17T11:41:41.452140Z",
- "iopub.status.idle": "2024-09-17T11:41:41.649897Z",
- "shell.execute_reply": "2024-09-17T11:41:41.648246Z"
+ "iopub.execute_input": "2024-09-17T14:03:28.246725Z",
+ "iopub.status.busy": "2024-09-17T14:03:28.245008Z",
+ "iopub.status.idle": "2024-09-17T14:03:28.492091Z",
+ "shell.execute_reply": "2024-09-17T14:03:28.490283Z"
},
"tags": []
},
@@ -106,14 +106,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:41,641 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:03:28,482 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:41,642 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.180899 s\n"
+ "2024-09-17 10:03:28,484 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.229596 s\n"
]
},
{
@@ -150,10 +150,10 @@
"id": "a7ab5fa3-e26b-47a7-818f-1bf367a55760",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:41:41.657111Z",
- "iopub.status.busy": "2024-09-17T11:41:41.656213Z",
- "iopub.status.idle": "2024-09-17T11:41:44.936237Z",
- "shell.execute_reply": "2024-09-17T11:41:44.934493Z"
+ "iopub.execute_input": "2024-09-17T14:03:28.499890Z",
+ "iopub.status.busy": "2024-09-17T14:03:28.498502Z",
+ "iopub.status.idle": "2024-09-17T14:03:32.097580Z",
+ "shell.execute_reply": "2024-09-17T14:03:32.095851Z"
},
"tags": []
},
@@ -162,14 +162,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:44,927 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:03:32,088 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:44,929 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.234838 s\n"
+ "2024-09-17 10:03:32,090 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.552542 s\n"
]
},
{
@@ -211,10 +211,10 @@
"id": "24043abc-1878-4e00-8229-36d4a0368b98",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:41:44.944127Z",
- "iopub.status.busy": "2024-09-17T11:41:44.942645Z",
- "iopub.status.idle": "2024-09-17T11:41:45.315757Z",
- "shell.execute_reply": "2024-09-17T11:41:45.313951Z"
+ "iopub.execute_input": "2024-09-17T14:03:32.104908Z",
+ "iopub.status.busy": "2024-09-17T14:03:32.103701Z",
+ "iopub.status.idle": "2024-09-17T14:03:32.391136Z",
+ "shell.execute_reply": "2024-09-17T14:03:32.389456Z"
},
"tags": []
},
@@ -223,14 +223,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:45,306 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:03:32,382 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:41:45,308 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.330425 s\n"
+ "2024-09-17 10:03:32,383 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.247521 s\n"
]
},
{
@@ -264,10 +264,10 @@
"id": "f6142f27-e8d1-453c-bfe2-2265d9ff1914",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:41:45.323295Z",
- "iopub.status.busy": "2024-09-17T11:41:45.322199Z",
- "iopub.status.idle": "2024-09-17T11:57:34.946511Z",
- "shell.execute_reply": "2024-09-17T11:57:34.944339Z"
+ "iopub.execute_input": "2024-09-17T14:03:32.398472Z",
+ "iopub.status.busy": "2024-09-17T14:03:32.397398Z",
+ "iopub.status.idle": "2024-09-17T14:19:27.640657Z",
+ "shell.execute_reply": "2024-09-17T14:19:27.638881Z"
},
"tags": []
},
@@ -276,14 +276,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:57:34,936 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:19:27,631 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:57:34,938 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 949.564382 s\n"
+ "2024-09-17 10:19:27,633 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 955.184133 s\n"
]
},
{
diff --git a/tutorials/mimiciv.html b/tutorials/mimiciv.html
index 54400ac..b77cb7c 100644
--- a/tutorials/mimiciv.html
+++ b/tutorials/mimiciv.html
@@ -615,7 +615,7 @@ Imports and instantiate
-2024-09-17 07:57:47,514 INFO cycquery.orm - Database setup, ready to run queries!
+2024-09-17 10:19:45,079 INFO cycquery.orm - Database setup, ready to run queries!
@@ -660,7 +660,7 @@ Example 1. Get all patient admissions from 2021 or later (approx year of adm
-2024-09-17 07:57:50,574 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:19:49,461 INFO cycquery.orm - Query returned successfully!
@@ -668,7 +668,7 @@ Example 1. Get all patient admissions from 2021 or later (approx year of adm
-2024-09-17 07:57:50,577 INFO cycquery.utils.profile - Finished executing function run_query in 0.672677 s
+2024-09-17 10:19:49,462 INFO cycquery.utils.profile - Finished executing function run_query in 1.986367 s
@@ -713,7 +713,7 @@ Example 2. Get all patient encounters with diagnoses (
-2024-09-17 07:58:06,130 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:19:58,610 INFO cycquery.orm - Query returned successfully!
@@ -721,7 +721,7 @@ Example 2. Get all patient encounters with diagnoses (
-2024-09-17 07:58:06,132 INFO cycquery.utils.profile - Finished executing function run_query in 15.477935 s
+2024-09-17 10:19:58,612 INFO cycquery.utils.profile - Finished executing function run_query in 9.072297 s
@@ -766,7 +766,7 @@ Example 3. Advanced - uses
-2024-09-17 07:58:09,912 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:20:02,401 INFO cycquery.orm - Query returned successfully!
@@ -774,7 +774,7 @@ Example 3. Advanced - uses
-2024-09-17 07:58:09,914 INFO cycquery.utils.profile - Finished executing function run_query in 3.710405 s
+2024-09-17 10:20:02,403 INFO cycquery.utils.profile - Finished executing function run_query in 3.719482 s
@@ -815,7 +815,7 @@ Example 4. Get routine vital signs for patients from year 2015.
-2024-09-17 07:58:14,094 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:20:07,692 INFO cycquery.orm - Query returned successfully!
@@ -823,7 +823,7 @@ Example 4. Get routine vital signs for patients from year 2015.
-2024-09-17 07:58:14,095 INFO cycquery.utils.profile - Finished executing function run_query in 4.107843 s
+2024-09-17 10:20:07,694 INFO cycquery.utils.profile - Finished executing function run_query in 5.219430 s
@@ -864,7 +864,7 @@ Example 5. Get hemoglobin lab tests for patients from year 2009.
-2024-09-17 07:58:19,169 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:20:13,117 INFO cycquery.orm - Query returned successfully!
@@ -872,7 +872,7 @@ Example 5. Get hemoglobin lab tests for patients from year 2009.
-2024-09-17 07:58:19,170 INFO cycquery.utils.profile - Finished executing function run_query in 5.003948 s
+2024-09-17 10:20:13,119 INFO cycquery.utils.profile - Finished executing function run_query in 5.352773 s
@@ -919,7 +919,7 @@ Example 6. Get radiology reports and filter on keywords
-2024-09-17 08:00:41,243 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:22:23,689 INFO cycquery.orm - Query returned successfully!
@@ -927,7 +927,7 @@ Example 6. Get radiology reports and filter on keywords
-2024-09-17 08:00:41,245 INFO cycquery.utils.profile - Finished executing function run_query in 142.013149 s
+2024-09-17 10:22:23,691 INFO cycquery.utils.profile - Finished executing function run_query in 130.509553 s
@@ -970,7 +970,7 @@ Example 7. Get all female patient encounters from year 2015, and return batc
-2024-09-17 08:00:42,508 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:22:24,839 INFO cycquery.orm - Query returned successfully!
@@ -978,7 +978,7 @@ Example 7. Get all female patient encounters from year 2015, and return batc
-2024-09-17 08:00:42,510 INFO cycquery.utils.profile - Finished executing function run_query in 1.160325 s
+2024-09-17 10:22:24,841 INFO cycquery.utils.profile - Finished executing function run_query in 1.047307 s
@@ -1006,7 +1006,7 @@ Example 8. Running a raw SQL string.
-2024-09-17 08:00:42,843 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:22:25,425 INFO cycquery.orm - Query returned successfully!
@@ -1014,7 +1014,7 @@ Example 8. Running a raw SQL string.
-2024-09-17 08:00:42,845 INFO cycquery.utils.profile - Finished executing function run_query in 0.013243 s
+2024-09-17 10:22:25,427 INFO cycquery.utils.profile - Finished executing function run_query in 0.013066 s
diff --git a/tutorials/mimiciv.ipynb b/tutorials/mimiciv.ipynb
index f4eace8..d37e63c 100644
--- a/tutorials/mimiciv.ipynb
+++ b/tutorials/mimiciv.ipynb
@@ -35,10 +35,10 @@
"id": "53009e6b",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:57:40.792524Z",
- "iopub.status.busy": "2024-09-17T11:57:40.791174Z",
- "iopub.status.idle": "2024-09-17T11:57:49.859254Z",
- "shell.execute_reply": "2024-09-17T11:57:49.857378Z"
+ "iopub.execute_input": "2024-09-17T14:19:36.401434Z",
+ "iopub.status.busy": "2024-09-17T14:19:36.400053Z",
+ "iopub.status.idle": "2024-09-17T14:19:47.431004Z",
+ "shell.execute_reply": "2024-09-17T14:19:47.429254Z"
},
"tags": []
},
@@ -47,7 +47,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:57:47,514 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-09-17 10:19:45,079 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
]
},
{
@@ -105,10 +105,10 @@
"id": "cdfadaa4-6fd6-4fd7-85cf-e012aa0799e1",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:57:49.867400Z",
- "iopub.status.busy": "2024-09-17T11:57:49.865999Z",
- "iopub.status.idle": "2024-09-17T11:57:50.585393Z",
- "shell.execute_reply": "2024-09-17T11:57:50.583355Z"
+ "iopub.execute_input": "2024-09-17T14:19:47.438751Z",
+ "iopub.status.busy": "2024-09-17T14:19:47.437162Z",
+ "iopub.status.idle": "2024-09-17T14:19:49.469880Z",
+ "shell.execute_reply": "2024-09-17T14:19:49.468209Z"
}
},
"outputs": [
@@ -116,14 +116,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:57:50,574 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:19:49,461 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:57:50,577 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.672677 s\n"
+ "2024-09-17 10:19:49,462 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.986367 s\n"
]
},
{
@@ -160,10 +160,10 @@
"id": "a89a9cf0",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:57:50.593280Z",
- "iopub.status.busy": "2024-09-17T11:57:50.591878Z",
- "iopub.status.idle": "2024-09-17T11:58:06.139655Z",
- "shell.execute_reply": "2024-09-17T11:58:06.137902Z"
+ "iopub.execute_input": "2024-09-17T14:19:49.476666Z",
+ "iopub.status.busy": "2024-09-17T14:19:49.476033Z",
+ "iopub.status.idle": "2024-09-17T14:19:58.619611Z",
+ "shell.execute_reply": "2024-09-17T14:19:58.617970Z"
}
},
"outputs": [
@@ -171,14 +171,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:58:06,130 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:19:58,610 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:58:06,132 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 15.477935 s\n"
+ "2024-09-17 10:19:58,612 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 9.072297 s\n"
]
},
{
@@ -225,10 +225,10 @@
"id": "03936cee",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:58:06.147113Z",
- "iopub.status.busy": "2024-09-17T11:58:06.146048Z",
- "iopub.status.idle": "2024-09-17T11:58:09.922410Z",
- "shell.execute_reply": "2024-09-17T11:58:09.920686Z"
+ "iopub.execute_input": "2024-09-17T14:19:58.627174Z",
+ "iopub.status.busy": "2024-09-17T14:19:58.625763Z",
+ "iopub.status.idle": "2024-09-17T14:20:02.410587Z",
+ "shell.execute_reply": "2024-09-17T14:20:02.408924Z"
}
},
"outputs": [
@@ -236,14 +236,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:58:09,912 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:20:02,401 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:58:09,914 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.710405 s\n"
+ "2024-09-17 10:20:02,403 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 3.719482 s\n"
]
},
{
@@ -290,10 +290,10 @@
"id": "56a72377",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:58:09.930492Z",
- "iopub.status.busy": "2024-09-17T11:58:09.928742Z",
- "iopub.status.idle": "2024-09-17T11:58:14.103225Z",
- "shell.execute_reply": "2024-09-17T11:58:14.101562Z"
+ "iopub.execute_input": "2024-09-17T14:20:02.417805Z",
+ "iopub.status.busy": "2024-09-17T14:20:02.416743Z",
+ "iopub.status.idle": "2024-09-17T14:20:07.701688Z",
+ "shell.execute_reply": "2024-09-17T14:20:07.700052Z"
}
},
"outputs": [
@@ -301,14 +301,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:58:14,094 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:20:07,692 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:58:14,095 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 4.107843 s\n"
+ "2024-09-17 10:20:07,694 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 5.219430 s\n"
]
},
{
@@ -351,10 +351,10 @@
"id": "bce11f81",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:58:14.110228Z",
- "iopub.status.busy": "2024-09-17T11:58:14.109204Z",
- "iopub.status.idle": "2024-09-17T11:58:19.177813Z",
- "shell.execute_reply": "2024-09-17T11:58:19.176459Z"
+ "iopub.execute_input": "2024-09-17T14:20:07.708799Z",
+ "iopub.status.busy": "2024-09-17T14:20:07.707719Z",
+ "iopub.status.idle": "2024-09-17T14:20:13.126408Z",
+ "shell.execute_reply": "2024-09-17T14:20:13.124688Z"
}
},
"outputs": [
@@ -362,14 +362,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:58:19,169 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:20:13,117 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 07:58:19,170 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 5.003948 s\n"
+ "2024-09-17 10:20:13,119 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 5.352773 s\n"
]
},
{
@@ -412,10 +412,10 @@
"id": "f00d270c-d78f-4dc0-8dae-ff4d52958c8b",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T11:58:19.185262Z",
- "iopub.status.busy": "2024-09-17T11:58:19.183893Z",
- "iopub.status.idle": "2024-09-17T12:00:41.253346Z",
- "shell.execute_reply": "2024-09-17T12:00:41.251442Z"
+ "iopub.execute_input": "2024-09-17T14:20:13.133401Z",
+ "iopub.status.busy": "2024-09-17T14:20:13.132517Z",
+ "iopub.status.idle": "2024-09-17T14:22:23.698456Z",
+ "shell.execute_reply": "2024-09-17T14:22:23.696776Z"
},
"tags": []
},
@@ -424,14 +424,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:00:41,243 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:22:23,689 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:00:41,245 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 142.013149 s\n"
+ "2024-09-17 10:22:23,691 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 130.509553 s\n"
]
},
{
@@ -480,10 +480,10 @@
"id": "28683d70-376e-4d9b-883d-1a7de634e455",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T12:00:41.260648Z",
- "iopub.status.busy": "2024-09-17T12:00:41.259680Z",
- "iopub.status.idle": "2024-09-17T12:00:42.821880Z",
- "shell.execute_reply": "2024-09-17T12:00:42.820131Z"
+ "iopub.execute_input": "2024-09-17T14:22:23.705677Z",
+ "iopub.status.busy": "2024-09-17T14:22:23.704761Z",
+ "iopub.status.idle": "2024-09-17T14:22:25.403816Z",
+ "shell.execute_reply": "2024-09-17T14:22:25.402075Z"
}
},
"outputs": [
@@ -491,14 +491,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:00:42,508 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:22:24,839 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:00:42,510 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.160325 s\n"
+ "2024-09-17 10:22:24,841 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.047307 s\n"
]
},
{
@@ -543,10 +543,10 @@
"id": "a853deec",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T12:00:42.829810Z",
- "iopub.status.busy": "2024-09-17T12:00:42.828560Z",
- "iopub.status.idle": "2024-09-17T12:00:42.852791Z",
- "shell.execute_reply": "2024-09-17T12:00:42.851087Z"
+ "iopub.execute_input": "2024-09-17T14:22:25.411741Z",
+ "iopub.status.busy": "2024-09-17T14:22:25.410443Z",
+ "iopub.status.idle": "2024-09-17T14:22:25.433909Z",
+ "shell.execute_reply": "2024-09-17T14:22:25.432306Z"
},
"tags": []
},
@@ -555,14 +555,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:00:42,843 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:22:25,425 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:00:42,845 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.013243 s\n"
+ "2024-09-17 10:22:25,427 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.013066 s\n"
]
},
{
diff --git a/tutorials/omop.html b/tutorials/omop.html
index 6bcf83d..173725e 100644
--- a/tutorials/omop.html
+++ b/tutorials/omop.html
@@ -623,7 +623,7 @@ Imports and instantiate
-2024-09-17 08:00:51,426 INFO cycquery.orm - Database setup, ready to run queries!
+2024-09-17 10:22:32,043 INFO cycquery.orm - Database setup, ready to run queries!
@@ -698,7 +698,7 @@ Example 1. Get all patient visits in or after 2010.
-2024-09-17 08:00:53,170 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:22:33,719 INFO cycquery.orm - Query returned successfully!
@@ -706,7 +706,7 @@ Example 1. Get all patient visits in or after 2010.
-2024-09-17 08:00:53,171 INFO cycquery.utils.profile - Finished executing function run_query in 0.490825 s
+2024-09-17 10:22:33,721 INFO cycquery.utils.profile - Finished executing function run_query in 0.452071 s
@@ -764,7 +764,7 @@ Example 2. Get measurements for all visits in or after 2020.
-2024-09-17 08:00:54,661 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:22:35,248 INFO cycquery.orm - Query returned successfully!
@@ -772,7 +772,7 @@ Example 2. Get measurements for all visits in or after 2020.
-2024-09-17 08:00:54,663 INFO cycquery.utils.profile - Finished executing function run_query in 1.271455 s
+2024-09-17 10:22:35,249 INFO cycquery.utils.profile - Finished executing function run_query in 1.150477 s
@@ -818,7 +818,7 @@ Imports and instantiate
-2024-09-17 08:01:02,271 INFO cycquery.orm - Database setup, ready to run queries!
+2024-09-17 10:22:42,209 INFO cycquery.orm - Database setup, ready to run queries!
@@ -858,7 +858,7 @@ Example 1. Get all patient visits that ended in a mortality outcome in or af
-2024-09-17 08:01:09,672 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:22:49,434 INFO cycquery.orm - Query returned successfully!
@@ -866,7 +866,7 @@ Example 1. Get all patient visits that ended in a mortality outcome in or af
-2024-09-17 08:01:09,674 INFO cycquery.utils.profile - Finished executing function run_query in 1.271381 s
+2024-09-17 10:22:49,436 INFO cycquery.utils.profile - Finished executing function run_query in 1.027628 s
@@ -922,7 +922,7 @@ Example 2. Get all measurements for female patient visits with
-2024-09-17 08:06:04,776 INFO cycquery.orm - Query returned successfully!
+2024-09-17 10:27:12,820 INFO cycquery.orm - Query returned successfully!
@@ -930,7 +930,7 @@ Example 2. Get all measurements for female patient visits with
-2024-09-17 08:06:04,779 INFO cycquery.utils.profile - Finished executing function run_query in 294.857821 s
+2024-09-17 10:27:12,822 INFO cycquery.utils.profile - Finished executing function run_query in 263.137625 s
@@ -956,9 +956,28 @@ Example 2. Get all measurements for female patient visits with
measurement_concept_name
-Body weight 51
-No matching concept 48
-Urine output 1
+Respiratory rate 52
+No matching concept 21
+Glasgow coma score motor 8
+Imipenem [Susceptibility] by Disk diffusion (KB) 1
+Trimethoprim+Sulfamethoxazole [Susceptibility] by Disk diffusion (KB) 1
+Nitrofurantoin [Susceptibility] by Disk diffusion (KB) 1
+Ciprofloxacin [Susceptibility] by Disk diffusion (KB) 1
+cefTRIAXone [Susceptibility] by Disk diffusion (KB) 1
+cefTAZidime [Susceptibility] by Disk diffusion (KB) 1
+levoFLOXacin [Susceptibility] by Disk diffusion (KB) 1
+Tobramycin [Susceptibility] by Disk diffusion (KB) 1
+Gentamicin [Susceptibility] by Disk diffusion (KB) 1
+Cefepime [Susceptibility] by Disk diffusion (KB) 1
+Piperacillin+Tazobactam [Susceptibility] by Disk diffusion (KB) 1
+Ampicillin [Susceptibility] by Disk diffusion (KB) 1
+Meropenem [Susceptibility] by Disk diffusion (KB) 1
+Cefuroxime Parenteral [Susceptibility] by Disk diffusion (KB) 1
+ceFAZolin [Susceptibility] by Disk diffusion (KB) 1
+Ampicillin+Sulbactam [Susceptibility] by Disk diffusion (KB) 1
+Piperacillin [Susceptibility] by Disk diffusion (KB) 1
+Bacteria identified in Blood product unit.autologous by Culture 1
+Bacteria identified in Urine by Culture 1
Name: count, dtype: int64[pyarrow]
diff --git a/tutorials/omop.ipynb b/tutorials/omop.ipynb
index b8e3235..a66e180 100644
--- a/tutorials/omop.ipynb
+++ b/tutorials/omop.ipynb
@@ -45,10 +45,10 @@
"id": "53009e6b",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T12:00:47.238513Z",
- "iopub.status.busy": "2024-09-17T12:00:47.237082Z",
- "iopub.status.idle": "2024-09-17T12:00:52.632208Z",
- "shell.execute_reply": "2024-09-17T12:00:52.630412Z"
+ "iopub.execute_input": "2024-09-17T14:22:29.405706Z",
+ "iopub.status.busy": "2024-09-17T14:22:29.404703Z",
+ "iopub.status.idle": "2024-09-17T14:22:33.219913Z",
+ "shell.execute_reply": "2024-09-17T14:22:33.218081Z"
}
},
"outputs": [
@@ -56,7 +56,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:00:51,426 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-09-17 10:22:32,043 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
]
},
{
@@ -151,10 +151,10 @@
"id": "3a3d9cb9-fe40-45b8-ba2f-8de52a3b7f4f",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T12:00:52.639669Z",
- "iopub.status.busy": "2024-09-17T12:00:52.638404Z",
- "iopub.status.idle": "2024-09-17T12:00:53.286524Z",
- "shell.execute_reply": "2024-09-17T12:00:53.284902Z"
+ "iopub.execute_input": "2024-09-17T14:22:33.227328Z",
+ "iopub.status.busy": "2024-09-17T14:22:33.226043Z",
+ "iopub.status.idle": "2024-09-17T14:22:33.992678Z",
+ "shell.execute_reply": "2024-09-17T14:22:33.990998Z"
}
},
"outputs": [
@@ -162,14 +162,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:00:53,170 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:22:33,719 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:00:53,171 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.490825 s\n"
+ "2024-09-17 10:22:33,721 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 0.452071 s\n"
]
},
{
@@ -227,10 +227,10 @@
"id": "030e2491-a7cc-42f3-a1ca-618212b3524c",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T12:00:53.293686Z",
- "iopub.status.busy": "2024-09-17T12:00:53.292647Z",
- "iopub.status.idle": "2024-09-17T12:00:54.670949Z",
- "shell.execute_reply": "2024-09-17T12:00:54.669215Z"
+ "iopub.execute_input": "2024-09-17T14:22:33.999318Z",
+ "iopub.status.busy": "2024-09-17T14:22:33.998433Z",
+ "iopub.status.idle": "2024-09-17T14:22:35.257270Z",
+ "shell.execute_reply": "2024-09-17T14:22:35.255516Z"
}
},
"outputs": [
@@ -238,14 +238,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:00:54,661 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:22:35,248 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:00:54,663 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.271455 s\n"
+ "2024-09-17 10:22:35,249 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.150477 s\n"
]
},
{
@@ -303,10 +303,10 @@
"id": "0622b3df-2864-4f32-bd98-806019f59c50",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T12:00:54.678256Z",
- "iopub.status.busy": "2024-09-17T12:00:54.677187Z",
- "iopub.status.idle": "2024-09-17T12:01:08.333104Z",
- "shell.execute_reply": "2024-09-17T12:01:08.331284Z"
+ "iopub.execute_input": "2024-09-17T14:22:35.264742Z",
+ "iopub.status.busy": "2024-09-17T14:22:35.263668Z",
+ "iopub.status.idle": "2024-09-17T14:22:48.338171Z",
+ "shell.execute_reply": "2024-09-17T14:22:48.336490Z"
},
"tags": []
},
@@ -315,7 +315,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:01:02,271 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
+ "2024-09-17 10:22:42,209 \u001b[1;37mINFO\u001b[0m cycquery.orm - Database setup, ready to run queries!\n"
]
},
{
@@ -357,10 +357,10 @@
"id": "40ff2e83-75e4-4119-aa33-26f95e63ddaa",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T12:01:08.340845Z",
- "iopub.status.busy": "2024-09-17T12:01:08.339468Z",
- "iopub.status.idle": "2024-09-17T12:01:09.680984Z",
- "shell.execute_reply": "2024-09-17T12:01:09.679140Z"
+ "iopub.execute_input": "2024-09-17T14:22:48.344923Z",
+ "iopub.status.busy": "2024-09-17T14:22:48.344320Z",
+ "iopub.status.idle": "2024-09-17T14:22:49.443113Z",
+ "shell.execute_reply": "2024-09-17T14:22:49.441464Z"
},
"tags": []
},
@@ -369,14 +369,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:01:09,672 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:22:49,434 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:01:09,674 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.271381 s\n"
+ "2024-09-17 10:22:49,436 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 1.027628 s\n"
]
},
{
@@ -419,10 +419,10 @@
"id": "46fd771c-5da7-4bce-aec7-08a5210a069b",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T12:01:09.687874Z",
- "iopub.status.busy": "2024-09-17T12:01:09.687207Z",
- "iopub.status.idle": "2024-09-17T12:06:04.787369Z",
- "shell.execute_reply": "2024-09-17T12:06:04.785397Z"
+ "iopub.execute_input": "2024-09-17T14:22:49.450585Z",
+ "iopub.status.busy": "2024-09-17T14:22:49.449296Z",
+ "iopub.status.idle": "2024-09-17T14:27:12.829453Z",
+ "shell.execute_reply": "2024-09-17T14:27:12.827718Z"
},
"tags": []
},
@@ -431,14 +431,14 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:06:04,776 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
+ "2024-09-17 10:27:12,820 \u001b[1;37mINFO\u001b[0m cycquery.orm - Query returned successfully!\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
- "2024-09-17 08:06:04,779 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 294.857821 s\n"
+ "2024-09-17 10:27:12,822 \u001b[1;37mINFO\u001b[0m cycquery.utils.profile - Finished executing function run_query in 263.137625 s\n"
]
},
{
@@ -488,10 +488,10 @@
"id": "d20a2581-f613-4ab8-9feb-3e84b8835db1",
"metadata": {
"execution": {
- "iopub.execute_input": "2024-09-17T12:06:04.795908Z",
- "iopub.status.busy": "2024-09-17T12:06:04.794029Z",
- "iopub.status.idle": "2024-09-17T12:06:04.813097Z",
- "shell.execute_reply": "2024-09-17T12:06:04.811215Z"
+ "iopub.execute_input": "2024-09-17T14:27:12.836813Z",
+ "iopub.status.busy": "2024-09-17T14:27:12.835425Z",
+ "iopub.status.idle": "2024-09-17T14:27:12.920682Z",
+ "shell.execute_reply": "2024-09-17T14:27:12.919012Z"
},
"tags": []
},
@@ -500,9 +500,28 @@
"data": {
"text/plain": [
"measurement_concept_name\n",
- "Body weight 51\n",
- "No matching concept 48\n",
- "Urine output 1\n",
+ "Respiratory rate 52\n",
+ "No matching concept 21\n",
+ "Glasgow coma score motor 8\n",
+ "Imipenem [Susceptibility] by Disk diffusion (KB) 1\n",
+ "Trimethoprim+Sulfamethoxazole [Susceptibility] by Disk diffusion (KB) 1\n",
+ "Nitrofurantoin [Susceptibility] by Disk diffusion (KB) 1\n",
+ "Ciprofloxacin [Susceptibility] by Disk diffusion (KB) 1\n",
+ "cefTRIAXone [Susceptibility] by Disk diffusion (KB) 1\n",
+ "cefTAZidime [Susceptibility] by Disk diffusion (KB) 1\n",
+ "levoFLOXacin [Susceptibility] by Disk diffusion (KB) 1\n",
+ "Tobramycin [Susceptibility] by Disk diffusion (KB) 1\n",
+ "Gentamicin [Susceptibility] by Disk diffusion (KB) 1\n",
+ "Cefepime [Susceptibility] by Disk diffusion (KB) 1\n",
+ "Piperacillin+Tazobactam [Susceptibility] by Disk diffusion (KB) 1\n",
+ "Ampicillin [Susceptibility] by Disk diffusion (KB) 1\n",
+ "Meropenem [Susceptibility] by Disk diffusion (KB) 1\n",
+ "Cefuroxime Parenteral [Susceptibility] by Disk diffusion (KB) 1\n",
+ "ceFAZolin [Susceptibility] by Disk diffusion (KB) 1\n",
+ "Ampicillin+Sulbactam [Susceptibility] by Disk diffusion (KB) 1\n",
+ "Piperacillin [Susceptibility] by Disk diffusion (KB) 1\n",
+ "Bacteria identified in Blood product unit.autologous by Culture 1\n",
+ "Bacteria identified in Urine by Culture 1\n",
"Name: count, dtype: int64[pyarrow]"
]
},